Structure and stability of the tetrahydridoselenonium dication,SeH4 2+

Ab initio molecular orbital theory with triple-zeta-valence plus polarization basis sets and with electron correlation incorporated at the fourth-order Møller-Plesset level has been used to study the tetrahydridoonium dications, OH₄ ²⁺, SH₄ ²⁺, and SeH₄ ²⁺. The tetrahydridoselenonium dication SeH₄ ²⁺ is predicted to have a tetrahedral (T _d )structure, similar to OH₄ ²⁺ and SH₄ ²⁺, with short bonds to hydrogen (1.483 Å). Although deprotonation of SeH₄ ²⁺ is thermodynamically favored Cby 104 kJ mol^–1), such a reaction is inhibited by a large barrier (240kJmol^–1]. Thus, SeH₄ ²⁺ lies in a deep potential well and as an isolated species should have a long lifetime in the gas phase. The estimated heat of formation, H° _f , for SeH₄ ²⁺ is very high (2483 kJ mol^–1], as is the case for OH₄ ²⁺ and SH₄ ²⁺. Of the group IV onium dications (OH₄ ²⁺, SH₄ ²⁺, and SeH₄ ²⁺), SeH₄ ²⁺ displays the greatest kinetic and thermodynamic stability toward proton loss. Substantial solvent stabilization is required in order to generate SeH₄ ²⁺ in solution.     

Features of the interactions between the methyl-CpG motif and the arginine residues on the surface of MBD proteins

Recognition of the methylated regions of the DNA plays an important role in the epigenetic processes. We analyze the interactions between the methylated DNA and the methyl-CpG-binding proteins using two models. The first model was built from a methylated or non-methylated cytosine, a guanine and an arginine residue in the experimental arrangement. We applied the M06L density functional method with a small, polarized double-ζ basis set for the geometry optimizations, and the MP2 method with polarized triple-ζ basis set for the energy calculations. The second model was built from two methylcytosines, guanines, guanidinium groups plus an additional carboxyl group in the experimental arrangement. We applied the B3LYP method with a small, polarized double-ζ basis set for the geometry optimizations and thermal corrections. The single-point energies were obtained from dual-hybrid dRPA75 and dRPA@PBE0 calculations supplemented by a moderately large polarized triple-ζ basis set. The hydration effects were modeled by adding explicit water molecules. These calculations revealed that the hydrophobic interaction has the largest contribution to the Gibbs interaction energy and turns the arginine side chains into hydrogen bonding position. Our results show that the translation of the protein along the DNA double helix is sterically hindered by the contact of its arginine side chains with the methyl groups of the methyl cytosines. This supports a hopping mechanism for the searching movement of the protein along the DNA.

     

Basis sets for molecular interactions. 2. Application to H3N?HF,H3N?HOH,H2O?HF, (NH3)2, and H3CH?OH2

Modifications of the standard 6-31G** basis set as recommended in the accompanying paper are found to markedly lower the basis set superposition error (BSSE) in the title complexes, in contrast to enlargement to a triple-ζ scheme or by addition of a diffuse sp shell or a second set of d-functions without prior optimization, all of which lead to BSSE increase. After appropriate correction for correlation and superposition effects, all basis sets (with the exception of the standard 6-31G** and 6-311G** with their very large BSSE) predict the cyclic geometry of NH₃ dimer to be more stable than the linear arrangement. Correlation and BSSE can shift the equilibrium intermolecular distance in H₃CH-OH₂ by up to 0.4 Å. Failure to correct for superposition error leads to a drastic exaggeration of both the SCF and MP2 components of the interaction energy in this complex. Much better estimates are furnished by our recommended basis sets with their smaller superposition errors.     

Basis set and correlation energy dependence of geometry and harmonic frequencies of difluoroethane,CHF2CH3

Optimum geometries and harmonic frequencies calculated at the Hartree–Fock and the MP2 level are reported for the fluorohydrocarbon CHF₂CH₃; basis sets employed range from STO-3G to 6-311G**. The significantly shortened C? C distance of 1.50 Å is reproduced already with the simplest split-valence basis set; the C? F distance of 1.36 Å on the other hand needs MP2 correction at least at the double-ζ or 6-311G* level. Symmetry coordinates defined in terms of internal coordinates are in qualitative agreement with available experimental evidence. Even the best basis set yields frequencies that differ from experimental (anharmonic) values by up to 200 cm^?1 indicating the well-known necessity of including higher-order force constants if quantitative agreement with experiment is to be achieved.     

High‐level ab initio study of the N+(3P)+SH2 reactions in the gas phase: Role of spin‐forbidden pathways

The singlet and triplet potential energy surfaces involved in N⁺+SH₂ reactions have been explored using high‐level ab initio techniques. The geometries of the stationary points were optimized at the QCISD/6‐311G(df,p) level. The final energies were obtained in CCSD(T)/6‐311+G(3df,2p) single‐point calculations. The results obtained show that, although the N⁺(¹D)+SH₂ entrance channel is higher in energy than the N⁺(³P)+SH₂ one, most of the [H₂, S, N]⁺ singlet state cations are lower in energy than the corresponding triplets, due to their different bonding characteristics. Both singlet and triplet potential energy surfaces are quite close each other, and crossover between them can occur. The minimum energy crossing points were located by means of CASSCF(6,5) calculations. The spin‐orbit couplings show that the transition probability from the triplet to the singlet potential energy surface is significantly large. One of the most important consequences is that some of the products of the reaction, such as SH⁺, can be formed in typical spin‐forbidden processes. Since all the relevant structures along these pathways are much lower in energy than the reactants, this mechanism should be accessible even at low impact energies and therefore could be important in processes taking place in interstellar media. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Ab Initio Study on the Mechanism of the Atmospheric Reaction OH+O3→HO2+O2

The atmospheric reaction (1) OH + O₃→HO₂ + O₂ was investigated theoretically by using MP2, QCISD, QCISD(T), and CCSD(T) methods with various basis sets. At the highest level of theory, namely, QCISD, the reaction is direct, with only one transition state between reactants and products. However, at the MP2 level, the reaction proceeds through a two‐step mechanism and shows two transition states, TS1 and TS2 , separated by an intermediate, Int . The different methodologies employed in this paper consistently predict the barrier height of reaction (1) to be within the range 2.16–5.11 kcal mol^?1, somewhat higher than the experimental value of 2.0 kcal mol^?1.     

On the kinetic stability of the SH3X species with X=F,Cl

Portions of the [S, H₃, X] (X=F, Cl) potential energy surfaces (PESs) were explored using the RHF, MP2, and QCISD(T) methods with emphasis on H₂ and HX eliminations, SH₃X→SHX+H₂ and SH₃X→SH₂+HX, respectively. Upon the halogen X substitution, the most favorable decomposition pathway of SH₄ went over to HX elimination, proceeding with a very low activation barrier of 6.9 (X=F) and 1.3 (X=Cl) kcal/mol. Moreover, the transition states (TSs) for H₂ elimination from SH₃X resembled the less favorable homopolar TS of SH₄. Upon the X=F substitution, the barrier to H₂ loss of SH₄ was calculated to increase from 19.5 to 21.5 kcal/mol. For X=Cl, only the indirect H₂ elimination path via the SH₂+HCl→SHCl+H₂ exchange was found. The hydrogen‐exchange reaction SH₂+HX→SH₂+HX was predicted to occur through formation of the hydrogen‐bonded complex XHSH₂ and with a relatively high barrier of 43.5 (X=F) and 38.5 (X=Cl) kcal/mol. FHSH₂ and ClHSH₂ were found to be the lowest energy species on the [S, H₃, F] and [S, H₃, Cl] PESs, lying 53.4 and 44.7 kcal/mol below SH₃F and SH₃Cl, respectively. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 37–43, 1999     

Basis set dependence of protonation reactions of NH3, OH2, and SH2

All basis sets, ranging in size from minimal STO-nG to polarized double-valence n-31G^*, correctly predict that NH₃ has a higher proton affinity than OH₂ and SH₂ but most reverse the known order of the latter two. 4–31G^* results are in good agreement with experiment with regard to absolute as well as relative proton affinities of all three molecules. Further enlargement of the basis set and inclusion of electron correlation leads to no significant improvement of the 4-3 1G^* results.     

Density functional theory study of Te(CN)2, Te(CN)(NC), and Te(NC)2 and their isomerizations

The equilibrium structures of Te(CN)₂, Te(CN)(NC), and Te(NC)₂ and three isomerization reactions: Te(CN)₂ ? Te(CN)(NC), Te(CN)(NC) ? Te(NC)₂, and Te(CN)₂ ? Te(NC)₂ were studied in the gas-phase using density functional theory. Three functionals (B3LYP, BLYP, and BHLYP) were employed to characterize the low-lying electronic singlet and triplet TeC₂N₂ isomers. The basis sets for carbon and nitrogen used were of double-ζ plus polarization quality with additional s- and p-type diffuse functions, DZP++. For the tellurium atom, the LANL2DZ (ECP) basis set was used. The energetic ordering (kcal mol^?1) (B3LYP) including zero-point vibrational energy corrections for the singlet ground state isomers follows: Te(CN)₂ (0.0, global minimum) < Te(CN)(NC) (15.4) < Te(NC)₂ (29.8). Electrostatic potentials and average local ionization energies of the ground state Te(CN)₂, Te(CN)(NC), and Te(NC)₂ isomers provide some guidance as to sites for noncovalent and covalent interactions. Energetics such as the different forms of electron affinities, ionization energies, and singlet–triplet gaps were also reported. Further the theoretical rate constants for the isomerization reactions were evaluated using transition state theory. We predict that these isomers may crystallize in similar patterns, if stable, as does Se(CN)₂.     

Basis set dependence of ab initio geometry predictions for AB4 molecules

Theoretical predictions of AB₄ molecular structures are very sensitive to choice of basis set. This has been previously demonstrated for the SH₄ and SF₄ molecules. Here it is shown that while both minimum and double zeta basis sets predict ClF₄⁺ to have a C_4v structure, the addition of d functions on Cl results in a C_2v geometry, similar to the experimentally known structure of SF₄.     

Energy-adjustedab initio pseudopotentials for the second and third row transition elements

Summary Nonrelativistic and quasirelativisticab initio pseudopotentials substituting the M^(Z–28)+-core orbitals of the second row transition elements and the M^(Z–60)+-core orbitals of the third row transition elements, respectively, and optimized (8s7p6d)/[6s5p3d]-GTO valence basis sets for use in molecular calculations have been generated. Additionally, corresponding spin-orbit operators have also been derived. Atomic excitation and ionization energies from numerical HF as well as from SCF pseudopotential calculations using the derived basis sets differ in most cases by less than 0.1 eV from corresponding numerical all-electron results. Spin-orbit splittings for lowlying states are in reasonable agreement with corresponding all-electron Dirac-Fock (DF) results.     

Scalar-relativistic 5f-in-core pseudopotentials and core-polarization potentials for trivalent actinides: calibration calculations for Ac<Superscript>3+</Superscript>, Cm<Superscript>3+</Superscript> and Lr<Superscript>3+</Superscript> complexes

The performance of recently proposed 5f-in-core pseudopotentials for the trivalent actinides was investigated in calculations for model complexes An³⁺L ⁿ⁻ for three selected actinides (An³⁺ = Ac³⁺, Cm³⁺, Lr³⁺) and eight simple ligands with atoms from the first three periods of the table of elements (L ⁿ⁻ = F⁻, Cl⁻, OH⁻, SH⁻, CO, NH₂⁻, H₂O, H₂S, NH₃). Results of Hartree-Fock and Coupled Cluster with singles, doubles and perturbative triples calculations using basis sets of quadruple-zeta quality are compared to corresponding reference data obtained with scalar-relativistic energy-adjusted 5f-in-valence small-core pseudopotentials. The inclusion of core-polarization potentials in the 5f-in-core pseudopotential calculations and corrections of the basis set superposition error by the counterpoise correction leads to very good agreement between the 5f-in-valence and 5f-in-core pseudopotential results for bond lengths, bond angles and binding energies. Results from 5f-in-core pseudopotential calculations using different density functionals also show reasonable agreement with the more rigorous Coupled Cluster results. It is argued that the An 5f rather than the An f population is a useful criterion for the applicability of a specific An 5f-in-core pseudopotential.     

Improved valence basis sets for divalent lanthanide 4f-in-core pseudopotentials

Improved energy-optimized (6s5p4d) and (7s6p5d) primitive valence basis sets have been derived for energy-consistent scalar-relativistic 4f-in-core pseudopotentials of the Stuttgart-Cologne variety modeling divalent lanthanides with a $4\hbox{f}^{n+1}$ occupation (n = 0?C13 for La?CYb). Segmented contracted basis sets covering the range of polarized double-, triple-, and quadruple-zeta quality, augmented by 2f1g correlation sets, were created for use in molecular calculations. The basis sets contain smaller (4s4p3d) and (5s5p4d) primitive subsets, which are designed in particular for solid state calculations of crystals containing divalent lanthanide ions. Hartree?CFock, density functional theory and coupled cluster results obtained with the new basis sets for lanthanide atomic ionization potentials as well as of geometry optimizations of various test molecules, i.e. selected lanthanide mono- and dihydrides, mono- and difluorides, and monooxides, show a satisfactory agreement with experimental data as well as with corresponding scalar-relativistic all-electron results. Core-polarization potentials are found to improve the results, especially for the atomic first and second ionization potentials.     

An Ab Initio Study on the Mechanism of the Atmospheric Reaction NH2+O3→H2NO+O2

The atmospheric reaction NH₂+O₃→H₂NO+O₂ has been investigated theoretically by using MP2, QCISD, QCISD(T), CCSD(T), CASSCF, and CASPT2 methods with various basis sets. At the MP2 level of theory, the hypersurface of the potential energy (HPES) shows a two step reaction mechanism. Therefore, the mechanism proceeds along two transition states (TS1 and TS2), separated by an intermediate designated as Int. However, when the single‐reference higher correlated QCISD and the multiconfigurational CASSCF methodologies have been employed, the minimum structure Int and TS2 are not found on the HPES, which thus confirms a direct reaction mechanism. Single‐reference high correlated and multiconfigurational methods consistently predict the barrier height of the reaction to be within the range of 3.9 to 6.6 kcal mol^?1, which is somewhat higher than the experimental value. ¹ The calculated reaction enthalpy is ?67.7 kcal mol^?1.     

Electronic and geometric structure analysis of neutral and anionic alkali metal complexes of the CX series (X = O,S, Se,Te, Po): The case of M(CX) n = 1–4 (M = Li,Na) and their dimers

Bonding mechanisms, potential energy curves, accurate structures, energetics, and electron affinities are obtained for all M(CX)_1–3 species with M = Li, Na, and X = O, S, Se, Te, and Po, at the coupled-cluster level with triple-ζ quality basis sets. We discuss and rationalize the trends within different molecular groups. For example, we found larger binding energies for M = Li, for CX = CPo, and for the tri-coordinated (n = 3) complexes. All three facts are explained by the fact that the global minimum of the titled complexes originate from the first excited ²P (2p¹ for Li or 3p¹ for Na) state of the metal, with each ligand forming a dative bond with the metal. All of the complexes, except Na(CO)₃, have stable anions, and their electron affinity increases as MCX < M(CX)₃ < M(CX)₂. This sequence is attributed to the binding modes of these complexes. The Li(CO)₃ and Li(CS)₃ complexes are able to accommodate a fourth ligand, which is attached to the system electrostatically. Finally, two Li(CO)₃ molecules can bind together covalently to make the ethane analog. The staggered conformer was found lower in energy and unlike ethane the CO ligands bend toward the neighboring Li(CO)₃ moiety. © 2019 Wiley Periodicals, Inc.     

Irreversibility,decay, and asymptotic dynamics

Ab initio molecular-orbital theory has been used to study the 1,3-sigmatropic hydrogen rearrangements: propene → propene, formic acic → formic acid, and vinyl alcohol → acetaldehyde. Fully optimized structures of stable molecules and transition states have been determined using gradient procedures and the 4-31G basis set. Improved energies have been obtained using a variety of techniques with basis sets up to the size of double-ζ plus polarization (DZP ) and electron correlation up to the CEPA /DZP level. Although both polarization functions and electron correlation lead to a lowering of the calculated barriers, the values remain substantial for all three rearrangements.     

Systematic study of the lowest energy states of Pd,Pd2, and Pd3

A systematic study has been carried out for the determination and characterization of the lowest states of Pd, Pd₂, and Pd₃ using some of the best ab initio tools available at present (conventional and DFT). Full electron ab initio calculations using the HF, MP2, MP3, MP4, and QCI methods were compared with DFT methods using several gradient-corrected functionals as well as the hybrid B3LYP functional that performed very well for the energetics studies of these small clusters. A suitable basis set has been found to perform considerably well with palladium atoms, another of double-ζ quality has been found insufficient to reproduce basic characteristics of the smallest palladium clusters. The results indicate that the ground state for Pd is a singlet. The dimer is a triplet; however, it is very difficult to ascertain due to the closeness between singlet and triplet states (0.9 kcal/mol). The trimer ground state was found to be a triplet with a separation from the lowest singlet of 3.2 kcal/mol. The lowest triplet and singlet of Pd₃ were practically equilateral triangles. © 1997 John Wiley & Sons, Inc.     

A theoretical study of the sulphonium cation SH+3

Ab initio Hartree—Fock calculations with STO-3G functions have been performed to determine the structure (1.371 Å and 95.33°) of SH⁺₃ and the proton affinity (≈196 kcal/mol) of H₂S. Inclusion of a sulphur 3d function in the basis has been found essential to give a better geometry of SH⁺₃.