Pople Style Basis Sets for the Calculation of NMR Spin–Spin Coupling Constants: the 6-31G-J and 6-311G-J Basis Sets

We present a modification of the small and popular Pople basis sets, 6-31G and 6-311G, for density functional theory calculations of Fermi contact dominated NMR indirect nuclear spin–spin coupling constants. These new basis sets, 6-31G-J and 6-311G-J, contain twice the number of contracted s-type functions but the same number of contracted p-type functions as the original Pople basis set. For our test set of 12 one-, two- and three-bond coupling constants, the new basis sets augmented with the standard diffuse and polarization functions, i.e., the 6-31+G*-J and 6-311++G**-J basis sets, lead to a maximum deviation of 5 and 2 Hz, respectively, compared to results obtained with the 6 or more times larger aug-pcJ-4 basis set. In correlated wave function calculations using the second-order polarization propagator approximation, the deviations with respect to the aug-ccJ-pVQZ basis set are 8 and 3 Hz and thus slightly larger

On the Angular Dependence of the Vicinal Fluorine−Fluorine Coupling Constant in 1,2-Difluoroethane: Deviation from a Karplus-like Shape

The angular dependence of the vicinal fluorine−fluorine coupling constant, 3JFF, for 1,2-difluoroethane has been investigated with several polarization propagator methods. 3JFF and its four Ramsey contributions were calculated using the random phase approximation (RPA), its multiconfigurational generalization, and both second-order polarization propagator approximations (SOPPA and SOPPA(CCSD)), using locally dense basis sets. The geometries were optimized for each dihedral angle at the level of density functional theory using the B3LYP functional and fourth-order Møller−Plesset perturbation theory. The resulting coupling constant curves were fitted to a cosine series with 8 coefficients. Our results are compared with those obtained previously and values estimated from experiment. It is found that the inclusion of electron correlation in the calculation of 3JFF reduces the absolute values. This is mainly due to changes in the FC contribution, which for dihedral angles around the trans conformation even changes its sign. This sign change is responsible for the breakdown of the Karplus-like curve

Kinetics and Thermodynamics of the Reaction between the ^•OH Radical and Adenine: A Theoretical Investigation

The accessibility of all possible reaction paths for the reaction between the nucleobase adenine and the ^•OH radical is investigated through quantum chemical calculations of barrier heights and rate constants at the ωB97X-D/6-311++G­(2df,2pd) level with Eckart tunneling corrections. First the computational method is validated by considering the hydrogen abstraction from the heterocyclic N₉ nitrogen in adenine as a test system. Geometries for all molecules in the reaction are optimized with four different DFT exchange-correlation functionals (B3LYP, BHandHLYP, M06-2X, and ωB97X-D), in combination with Pople and Dunning basis sets, all of which have been employed in similar investigations in the literature. Improved energies are obtained through single point calculations with CCSD­(T) and the same basis sets, and reaction rate constants are calculated for all methods both without tunneling corrections and with the Wigner, Bell, and Eckart corrections. In comparison to CCSD­(T)//BHandHLYP/aug-cc-pVTZ reference results, the ωB97X-D/6-311++G­(2df,2pd) method combined with Eckart tunneling corrections provides a sensible compromise between accuracy and time. Using this method, all subreactions of the reaction between adenine and the ^•OH radical are investigated. The total rate constants for hydrogen abstraction and addition for adenine are predicted with this method to be 1.06 × 10^–12 and 1.10 × 10^–12 cm³ molecules^–1 s^–1, respectively. Abstractions of H₆₁ and H₆₂ contribute the most, while only addition to the C₈ carbon is found to be of any significance, in contrast to previous claims that addition is the dominant reaction pathway. The overall rate constant for the complete reaction is found to be 2.17 × 10^–12 cm³ molecules^–1 s^–1, which agrees exceptionally well with experimental results

Importance of Triples Contributions to NMR Spin–Spin Coupling Constants Computed at the CC3 and CCSDT Levels

We present the first analytical implementation of CC3 second derivatives using the spin-unrestricted approach. This allows, for the first time, the calculation of nuclear spin–spin coupling constants (SSCC) relevant to NMR spectroscopy at the CC3 level of theory in a fully analytical manner. CC3 results for the SSCCs of a number of small molecules and their fluorine substituted derivatives are compared with the corresponding coupled cluster singles and doubles (CCSD) results obtained using specialized basis sets. For one-bond couplings the change when going from CCSD to CC3 is typically 1–3%, but much higher corrections were found for ¹<i>J</i>_CN in FCN, 15.7%, and ¹<i>J</i>_OF in OF₂, 6.4%. The changes vary significantly in the case of multibond couplings, with differences of up to 10%, and even 13.6% for ³<i>J</i>_FH in fluoroacetylene. Calculations at the coupled cluster singles, doubles, and triples (CCSDT) level indicate that the most important contributions arising from connected triple excitations in the coupled cluster expansion are accounted for at the CC3 level. Thus, we believe that the CC3 method will become the standard approach for the calculation of reference values of nuclear spin–spin coupling constants

Definitive Benchmark Study of Ring Current Effects on Amide Proton Chemical Shifts

The ring current effect on chemical shifts of amide protons (ΔδRC) is computed at the B3LYP/6-311++G(d,p)//B3LYP/aug-cc-pVTZ level of theory for 932 geometries of dimers of N-methylacetamide and aromatic amino acid side chains extracted from 21 different proteins. These ΔδRC values are scaled by 1.074, based on MP2/cc-pVQZ//B3LYP/aug-cc-pVTZ chemical shift calculations on four representative formamide/benzene dimers, and are judged to be accurate to within 0.1 ppm based on CCSD(T)/CBS//B3LYP/aug-cc-pVTZ calculations on formamide. The 932 scaled ΔδRC values are used to benchmark three empirical ring current models, including the Haigh–Mallion model used in the SPARTA, SHIFTX, and SHIFTS chemical shift prediction codes. Though the RMSDs for these three models are below 0.1 ppm, deviations up to 0.29 ppm are found, but these can be decreased to below 0.1 ppm by changing a single parameter. The simple point-dipole model is found to perform just as well as the more complicated Haigh–Mallion and Johnson–Bovey models

Optimized Basis Sets for Calculation of Electron Paramagnetic Resonance Hyperfine Coupling Constants: aug-cc-pVTZ-J for the 3d Atoms Sc–Zn

The hyperfine coupling tensor of electron paramagnetic resonance (EPR), describing the interaction between an electron and a given nuclei, depends strongly on the electron density at the nucleus. With standard Gaussian-type orbital basis sets (GTOs), employed in most calculations, it is difficult to obtain converged results of the hyperfine coupling tensor, and basis sets with more flexible core regions have therefore been devised. To this class of core property basis sets belong the aug-cc-pVTZ-J basis sets developed for the s- and p-block atoms. Here, we extend the aug-cc-pVTZ-J basis sets to include the 3d elements Sc–Zn. The converged optimal basis sets are throughout the series described by a (25s17p10d3f2g)/[17s10p7d3f2g] contraction scheme, where four tight s-, one tight p-, and one tight d-type function have been added to the original aug-cc-pVTZ basis sets. The basis sets are generally contracted, and molecular orbital coefficients are used as contraction coefficients. By validation studies with different functionals and compounds, it is shown that the values of the contraction coefficient are effectively independent of the compound used in their generation and the exchange-correlation functional employed in the calculation

On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in water

<p>The method and basis set dependence of zero-point vibrational corrections (ZPVCs) to nuclear magnetic resonance shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree–Fock, second-order Møller–Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn–Sham density functional theory with the B3LYP exchange-correlation functional methods in combination with the second-order vibrational perturbation theory (VPT2) approach for the vibrational corrections. As basis sets, the correlation consistent basis sets cc-pVXZ, aug-cc-pVXZ, cc-pCVXZ and aug-cc-pCVXZ with <i>X</i> = D, T, Q, 5, 6 and the polarisation consistent basis sets aug-pc-n and aug-pcS-n with <i>n</i> = 1, 2, 3, 4 were employed. Our results show that basis set convergence of the vibrational corrections is not monotonic and that very large basis sets are needed before a reasonable extrapolation to the basis set limit can be performed. Furthermore, our results suggest that coupled cluster methods and a decent basis set are required before the error of the electronic structure approach is lower than the inherent error of the VPT2 approximation.</p> <p></p

Ligand Sphere Conversions in Terminal Carbide Complexes

Metathesis is introduced as a preparative route to terminal carbide complexes. The chloride ligands of the terminal carbide complex [RuC­(Cl)₂(PCy₃)₂] (<b>RuC</b>) can be exchanged, paving the way for a systematic variation of the ligand sphere. A series of substituted complexes, including the first example of a cationic terminal carbide complex, [RuC­(Cl)­(CH₃CN)­(PCy₃)₂]⁺, is described and characterized by NMR, MS, X-ray crystallography, and computational studies. The experimentally observed irregular variation of the carbide ¹³C chemical shift is shown to be accurately reproduced by DFT, which also demonstrates that details of the coordination geometry affect the carbide chemical shift equally as much as variations in the nature of the auxiliary ligands. Furthermore, the kinetics of formation of the sqaure pyramidal dicyano complex, <i>trans</i>-[RuC­(CN)₂(PCy₃)₂], from <b>RuC</b> has been examined and the reaction found to be quite sluggish and of first order in both <b>RuC</b> and cyanide with a rate constant of <i>k</i> = 0.0104(6) M^–1 s^–1. Further reaction with cyanide leads to loss of the carbide ligand and formation of <i>trans</i>-[Ru­(CN)₄(PCy₃)₂]^2–, which was isolated and structurally characterized as its PPh₄⁺ salt

Analysis of the interactions in FCCF:(H₂O) and FCCF:(H₂O)₂ complexes through the study of their indirect spin–spin coupling constants

<p>A theoretical study of FCCF:(H₂O)<i>_n</i> complexes, with <i>n</i> = 1 and 2, has been carried out by means of ab initio computational methods. Three kinds of interactions are observed in the complexes: H···<i>π</i> and H···F hydrogen bonds and O···FC tetrel bonds. The indirect spin–spin coupling constants have been calculated at the CCSD/aug-cc-pVTZ-J computational level. Special attention has been paid to the dependence of the different intramolecular coupling constants in FCCF on the distance between the coupled nuclei and the presence or absence of water molecules. The exceptional sensitivity shown by these coupling constants to the presence of water molecules is quite notorious and can provide information on the bonding structure of the molecule.</p

An Isofagomine Analogue with an Amidine at the Pseudoanomeric Position

(3R,4R,5R)-2-Imino-3,4-dihydroxy-5-hydroxymethylpiperidine hydrocloride or isofagomidine was synthesized from d-arabinose in 12 steps and an overall yield of 9.9%. The synthesis proceeded by introduction of an aminomethyl group in the 4-position of d-arabinose and conversion of C-1 into a nitrile. The key step in the synthesis was a copper-catalyzed cyclization of aminonitrile to amidine. Isofagomidine was a potent α-mannosidase inhibitor (Ki = 0.75 μM)