New nonsymmetric P(OH)3 species. Comparison with the C3 isomer and themochemistry at the DFT, MP2, and CCSD(T) levels of theory

Two new less-symmetric P(OH)3 isomers that are more stable than the C3 structure are found at the density functional theory (B3PW91, B3LYP), MP2, and CCSD(T) levels with the large aug-cc-pvdz/pvtz basis sets. The C1 and C3 structures are qualitatively different from those found for the As(OH)3 molecule. An additional lower lying P(OH)3 structure with Cs symmetry has been obtained. With the largest basis set the Cs isomer is predicted to be the most stable. However, the inclusion of zero-point-energy corrections induces an inversion between the Cs and C1 isomers, with the latter becoming the lowest energy structure at the highest correlated level. Increasing inclusion of electronic correlation effects reduces the energy difference between the C1 and Cs structures while the C1-C3 energy difference and C1-Cs interconversion barrier become larger. In all cases, energy differences and barrier heights are around 1 kcal/mol.     

A New Nonsymmetric As(OH)3 Species. Comparison with the Known C3 Species and Thermochemistry at the HF,DFT(B3LYP), MP2, MP4, and CCSD(T) Levels of Theory.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.     

On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level

The geometries and interaction energies of stacked and hydrogen-bonded uracil dimers and a stacked adeninecdots, three dots, centeredthymine pair were studied by means of high-level quantum chemical calculations. Specifically, standard as well as counterpoise-corrected optimizations were performed at second-order Moller-Plesset (MP2) and coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)] levels with various basis sets up to the complete basis set limit. The results can be summarized as follows: (i) standard geometry optimization with small basis set (e.g., 6-31G(*)) provides fairly reasonable intermolecular separation; (ii) geometry optimization with extended basis sets at the MP2 level underestimates the intermolecular distances compared to the reference CCSD(T) results, whereas the MP2/cc-pVTZ counterpoise-corrected optimization agrees well with the reference geometries and, therefore, is recommended as a next step for improving MP2/cc-pVTZ geometries; (iii) the stabilization energy of stacked nucleic acids base pairs depends considerably on the method used for geometry optimization, so the use of reliable geometries, such as counterpoise-corrected MP2/cc-pVTZ ones, is recommended; (iv) the density functional theory methods fail completely in locating the energy minima for stacked structures and when the geometries from MP2 calculations are used, the resulting stabilization energies are strongly underestimated; (v) the self-consistent charges-density functional tight binding method, with inclusion of the empirical dispersion energy, accurately reproduces interaction energies and geometries of dispersion-bonded (stacked) complexes; this method can thus be recommended for prescanning the potential energy surfaces of van der Waals complexes.     

Revealing the physical nature and the strength of charge‐inverted hydrogen bonds by SAPT(DFT), MP2, SCS‐MP2, MP2C,and CCSD(T) methods

The physical nature of charge‐inverted hydrogen bonds in H₃XH YH₃ (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)‐based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS‐MP2, MP2C, and CCSD(T) methods utilizing dimer‐centered aug‐cc‐pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge‐inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: . It is confirmed that the aug‐cc‐pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole‐ζ quality. Considerably large binding energies suggest potential usefulness of charge‐inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ‐ and π‐hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge‐inverted hydrogen bond would become the first described case of a hydride‐triel bond. © 2017 Wiley Periodicals, Inc.     

OH+ C2H2N←C2H3 + NO→CH3 + NCO反应机理的密度泛函理论研究

应用密度泛函理论研究了反应通道(a)C2H3 NO→CH3 NCO和(b)C2H3 NO→OH C2H2N的反应机理．在B3LYP／6-31G(d)水平上优化了反应物、中间体、过滤态、产物的几何构型，通过频率分析确定了11个中间体和10个过渡态．所有的反应物、中间体、过渡态、产物都在CCSD／6-311 G(d，P)水平上进行了单点能较正．并讨论了反应的异构化过程．计算结果表明10是能量最低的中间体，比反应物的能量低308．479kJ／mol；过渡态1／3，2／5，3／4，4／8比反应物的能量高，其中3／4是能量最高的过渡态，比反应物的能量高91．894kJ／mol．通道(a)和(b)的理论放热值分别为111．059和96．619kJ／mol．     

Comparative study of BSSE correction methods at DFT and MP2 levels of theory

A comparative study of intermolecular potential energy curves is performed on the complexes H₂O(SINGLE BOND)HF, H₂O(SINGLE BOND)H₂O, H₂O(SINGLE BOND)H₂S, and H₂S(SINGLE BOND)H₂S using nine different basis sets at the MP2 and DFT (BLYP and B3LYP) levels of theory. The basis set superposition error is corrected by means of the counterpoise scheme and based on the “chemical Hamiltonian approach.” The counterpoise and CHA-corrected DFT curves are generally close to each other. Using small basis sets, the B3LYP functional cannot be favored against the BLYP one because the BLYP results sometimes get closer to the MP2 values than those of B3LYP. From the results—including the available literature data—we suggest that one has to use at least polarized-valence triple-zeta-quality basis sets (TZV, 6-311G) for the investigation of hydrogen-bonded complexes. Special attention must be paid to the physical nature of the binding. If the dispersion forces become significant DFT methods are not able to describe the interaction. Proper correction for the basis set superposition error is found to be mandatory in all cases. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 575–584, 1998     

Halogen‐Bonding Interactions with π Systems: CCSD(T), MP2, and DFT Calculations

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X=F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller–Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.     

New framework connectivity patterns in templated networks: the creatinine zinc phosphites C4N3OH7.ZnHPO3, C4N3OH7.Zn(H2O)HPO3, and (C4N3OH7)2.ZnHPO3.H2O

The syntheses, crystal structures, and properties of C(4)N(3)OH(7).ZnHPO(3), C(4)N(3)OH(7).Zn(H(2)O)HPO(3), and (C(4)N(3)OH(7))(2).ZnHPO(3).H(2)O are reported. These new creatinine zinc phosphites are built up from networks of vertex-sharing HPO(3) pseudopyramids and various types of ZnO(2)N(2), ZnO(3)N, and ZnO(2)N(H(2)O) tetrahedra, resulting in extended structures of different dimensionalities (as sheets, clusters, and chains, respectively). They demonstrate the structural effect of incorporating "terminal" (nonnetworking) Zn-N and Zn-OH(2) moieties into zinc centers. Crystal data: C(4)N(3)OH(7).ZnHPO(3), triclinic, P1 (No. 2), a = 8.9351(4) A, b = 9.5011(4) A, c = 9.9806(4) A, alpha = 87.451(1) degrees, beta = 85.686(1) degrees, gamma = 89.551(1) degrees, Z = 4; C(4)N(3)OH(7).Zn(H(2)O)HPO(3), monoclinic, P2(1)/c (No. 14), a = 10.1198(7) A, b = 7.2996(5) A, c = 13.7421(9) A, beta = 107.522(1) degrees, Z = 4; (C(4)N(3)OH(7))(2).ZnHPO(3).H(2)O, triclinic, P1 (No. 2), a = 10.7289(6) A, b = 10.9051(6)A, c = 13.9881(8) A, alpha = 89.508(1) degrees, beta = 74.995(1) degrees, gamma = 74.932(1) degrees, Z = 4.     

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.     

Stationary points on the energy hypersurface of the reaction O3 + H•→ [•O3H]* ⇆ O2 + •OH and thermodynamic functions of •O3H at G3MP2B3, CCSD(T)-CBS (W1U) and MR-ACPF-CBS levels of theory

The relative enthalpies, ΔH^o (0) and ΔH^o (298.15), of stationary points (four minimum and three transition structures) on the ^•O₃H potential energy surface were calculated with the aid of the G3MP2B3 as well as the CCSD(T)–CBS (W1U) procedures from which we earlier found mean absolute deviations (MAD) of 3.9 kJ mol⁻¹ and 2.3 kJ mol⁻¹, respectively, between experimental and calculated standard enthalpies of the formation of a set of 32 free radicals. For CCSD(T)-CBS (W1U) the well depth from O₃ + H^• to trans-^•O₃H, ΔH^o_well(298.15) = −339.1 kJ mol⁻¹, as well as the reaction enthalpy of the overall reaction O₃ + H^•→O₂ + ^•OH, Δ_rH^o(298.15) = −333.7 kJ mol⁻¹, and the barrier of bond dissociation of trans-^•O₃H → O₂ + ^•OH, ΔH^o(298.15) = 22.3 kJ mol⁻¹, affirm the stable short-lived intermediate ^•O₃H. In addition, for radicals cis-^•O₃H and trans-^•O₃H, the thermodynamic functions heat capacity C^o_p(T), entropy S^o (T), and thermal energy content H^o(T) − H^o(0) are tabulated in the range of 100 − 3000 K. The much debated calculated standard enthalpy of the formation of the trans-^•O₃H resulted to be Δ_fH^o(298.15) = 31.1 kJ mol ⁻¹ and 32.9 kJ mol ⁻¹, at the G3MP2B3 and CCSD(T)-CBS (W1U) levels of theory, respectively. In addition, MR-ACPF-CBS calculations were applied to consider possible multiconfiguration effects and yield Δ_fH^o(298.15) = 21.2 kJ mol ⁻¹. The discrepancy between calculated values and the experimental value of −4.2 ± 21 kJ mol⁻¹ is still unresolved. Note added in proof: Yu-Ran Luo and J. Alistair Kerr, based on the discussion in reference 12, recently presented an experimental value of Δ_fH^o(298.15) = 29.7 ± 8.4 kJ mol⁻¹ in the 85th edition of the CRC Handbook of Chemistry and Physics (in progress).     

Peptide models. XXXIII. Extrapolation of low-level Hartree-Fock data of peptide conformation to large basis set SCF,MP2, DFT,and CCSD(T) results. The Ramachandran surface of alanine dipeptide computed at various levels of theory

At the dawn of the new millenium, new concepts are required for a more profound understanding of protein structures. Together with NMR and X-ray-based 3D-structure determinations in silico methods are now widely accepted. Homology-based modeling studies, molecular dynamics methods, and quantum mechanical approaches are more commonly used. Despite the steady and exponential increase in computational power, high level ab initio methods will not be in common use for studying the structure and dynamics of large peptides and proteins in the near future. We are presenting here a novel approach, in which low- and medium-level ab initio energy results are scaled, thus extrapolating to a higher level of information. This scaling is of special significance, because we observed previously on molecular properties such as energy, chemical shielding data, etc., determined at a higher theoretical level, do correlate better with experimental data, than those originating from lower theoretical treatments. The Ramachandran surface of an alanine dipeptide now determined at six different levels of theory [RHF and B3LYP 3-21G, 6-31+G(d) and 6-311++G(d,p)] serves as a suitable test. Minima, first-order critical points and partially optimized structures, determined at different levels of theory (SCF, DFT), were completed with high level energy calculations such as MP2, MP4D, and CCSD(T). For the first time three different CCSD(T) sets of energies were determined for all stable B3LYP/6-311++G(d,p) minima of an alanine dipeptide. From the simplest ab initio data (e.g., RHF/3-21G) to more complex results [CCSD(T)/6-311+G(d,p)//B3LYP/6-311++G(d,p)] all data sets were compared, analyzed in a comprehensive manner, and evaluated by means of statistics.     

The electron affinities of transition metal atoms at the CCSD(T) and density functional levels of theory

 The electron affinities of Ti, V, Cr, Fe, Co, Ni, and Cu are computed using the density function theory and CCSD(T) approaches. Overall the CCSD(T) approach yields the best results. For this property, the B3LYP, BLYP, and BP86 functionals perform better than the BPW91, PBEPBE, and PBE1PBE ones. The accuracy of all the methods is higher if the number of 3delectrons is the same in the neutral atom and the anion. This is especially true for the density functional theory methods. Received: 23 January 2002 / Accepted: 1 April 2002 / Published online: 24 June 2002     

Stabilisation energy of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels

Stabilisation energies of stacked structures of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, CN) complexes were determined at the CCSD(T) complete basis set (CBS) limit level. These energies were constructed from MP2/CBS stabilisation energies and a CCSD(T) correction term determined with a medium basis set (6-31G**). The former energies were extrapolated using the two-point formula of Helgaker et al. from aug-cc-pVDZ and aug-cc-pVTZ Hartree-Fock energies and MP2 correlation energies. The CCSD(T) correction term is systematically repulsive. The final CCSD(T)/CBS stabilisation energies are large, considerably larger than previously calculated and increase in the series as follows: hexafluorobenzene (6.3 kcal mol(-1)), hexachlorobenzene (8.8 kcal mol(-1)), hexabromobenzene (8.1 kcal mol(-1)) and hexacyanobenzene (11.0 kcal mol(-1)). MP2/SDD** relativistic calculations performed for all complexes mentioned and also for benzene[dot dot dot]hexaiodobenzene have clearly shown that due to relativistic effects the stabilisation energy of the hexaiodobenzene complex is lower than that of hexabromobenzene complex. The decomposition of the total interaction energy to physically defined energy components was made by using the symmetry adapted perturbation treatment (SAPT). The main stabilisation contribution for all complexes investigated is due to London dispersion energy, with the induction term being smaller. Electrostatic and induction terms which are attractive are compensated by their exchange counterparts. The stacked motif in the complexes studied is very stable and might thus be valuable as a supramolecular synthon.     

Cu4(CH3C(OH)(PO3)2)2(C4H4N2)(H2O)4: a novel,three-dimensional copper diphosphonate with metamagnetism

A novel, three-dimensional copper diphosphonate Cu4(CH3C(OH)(PO3)2)2(C4H4N2)(H2O)4 (1) incorporating an organic pyrazine ligand has been hydrothermally synthesized, which exhibits antiferromagnetic ordering below 4.2 K and metamagnetic behavior.     

A Comparison of the Interacting Quantum Atoms (IQA) Analysis of the Two-Particle Density-Matrices of MP4SDQ and CCSD

Within the quantum topological energy partitioning method called Interacting Quantum Atoms (IQA) we transition from Møller-Plesset (MP4SDQ) to CCSD in calculating intra- and interatomic electron correlation energies for a set of hydrides, diatomics, a few simple molecules and non-covalently bonded complexes, using the uncontracted basis set 6-31++G(2d,2p). CCSD-IQA allows a more rigorous analysis of atomic electron correlation than that offered by Møller-Plesset, which returns IQA contributions that are identical to Hartree–Fock counterparts except for two-electron terms. The CCSD-IQA analysis returns bond and other interatomic correlation energies that are typically much larger in magnitude than the MP4SDQ values. Crisp patterns of energy transferability are detected in water clusters, both for intra-atomic and interatomic correlation energies. CCSD determines that the intra-atomic correlation energy of an oxygen drops by 15 kJ · mol^–1 for donating a hydrogen and by 25 kJ · mol^–1 for accepting a hydrogen.     

C(4)N(3)OH(7).Zn(H2O)HPO4, a neutral zincophosphate cluster

C(4)N(3)OH(7).Zn(H(2)O)HPO(4), built up from 4-rings of ZnO(2)(H(2)O)N and HPO(4) tetrahedra, is the first neutral, molecular, zincophosphate cluster. The unit-cell packing involves numerous O-H...O and N-H...O hydrogen bonds and pi...pi stacking interactions. Crystal data: C(4)N(3)OH(7).Zn(H(2)O)HPO(4), M(r) = 292.49, triclinic, P1 (No. 2), a = 9.2956(5) A, b = 11.2077(6) A, c = 19.8319(12) A, alpha = 80.314(1) degrees, beta = 78.829(1) degrees, gamma = 89.241(1) degrees, V = 1997.7(2) A(3), Z = 4.     

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