Computational Protocol to Evaluate Side-Chain Vicinal Spin-Spin Coupling Constants and Karplus Equation in Amino Acids: Alanine Dipeptide Model.

A computational protocol has been applied to the alanine dipeptide model in order to study the side-chain conformation, the calculated spin-spin coupling constants involved in the side-chain χ1 angle, and theoretical extended Karplus equations developed for amino acids. Two structures within the backbone secondary conformation are used to predict coupling constants which in addition are employed to analyze the effect of those structures on the resulting Karplus extended equations. The number of Fourier coefficients to be included within the Karplus equations is critically analyzed. Wave function and density functional methods as well as different basis sets are compared to find appropriate Karplus coefficients in the most efficient way. The influence of exchange and correlation functionals and the solvent effect on the calculated couplings are considered.

Performance of wave function and density functional methods for water hydrogen bond spin-spin coupling constants.

Spin-spin coupling constants in water monomer and dimer have been calculated using several wave function and density functional-based methods. CCSD, MCSCF, and SOPPA wave functions methods yield similar results, specially when an additive approach is used with the MCSCF. Several functionals have been used to analyze their performance with the Jacob's ladder and a set of functionals with different HF exchange were tested. Functionals with large HF exchange appropriately predict 1 J O H , 2 J H H and 2h J O O couplings, while 1h J O H is better calculated with functionals that include a reduced fraction of HF exchange. Accurate functionals for 1 J O H and 2 J H H have been tested in a tetramer water model. The hydrogen bond effects on these intramolecular couplings are additive when they are calculated by SOPPA(CCSD) wave function and DFT methods. Graphical Abstract Evaluation of the additive effect of the hydrogen bond on spin-spin coupling constants of water using WF and DFT methods.

Towards quantifying the role of exact exchange in the prediction hydrogen bond spin-spin coupling constants involving fluorine.

The effect of a fraction of Hartree-Fock exchange on the calculated spin-spin coupling constants involving fluorine through a hydrogen bond is analyzed in detail. Coupling constants calculated using wavefunction methods are revisited in order to get high-level calculations using the same basis set. Accurate MCSCF results are obtained using an additive approach. These constants and their contributions are used as a reference for density functional calculations. Within the density functional theory, the Hartree-Fock exchange functional is split in short- and long-range using a modified version of the Coulomb-attenuating method with the SLYP functional as well as with the original B3LYP. Results support the difficulties for calculating hydrogen bond coupling constants using density functional methods when fluorine nuclei are involved. Coupling constants are very sensitive to the Hartree-Fock exchange and it seems that, contrary to other properties, it is important to include this exchange for short-range interactions. Best functionals are tested in two different groups of complexes: those related with anionic clusters of type [F(HF)n](-) and those formed by difluoroacetylene and either one or two hydrogen fluoride molecules.

Dynamics of the O + ClO reaction: reactive and vibrational relaxation processes.

Classical trajectories have been integrated to study the O + ClO reaction, both reactive and vibrational energy transfer processes, for the range of temperatures 100 ≤ T/K ≤ 500 using momentum Gaussian binning. The employed potential energy surface is the recently proposed single-sheeted double many-body expansion potential energy surface for the (2)A" ground-state of ClO2 based on multireference ab initio data. A capture-type regime with a room-temperature rate constant of (17.8 ± 0.5) × 10(-12) cm(3) s(-1) and temperature dependence of k(T/K)/cm(3) s(-1) = 22.4 × 10(-12) × T(-0.81) exp(-39.2/T) has been found. Although the value reported here is half of the experimental and recommended one, tentative explanations are given. Other dynamical attributes are also examined for the title reaction, with state-to-all and state-to-state vibrational relaxation and excitation rate constants reported for temperatures of relevance in stratospheric chemistry.

Single-sheeted double many-body expansion potential energy surface for ground-state ClO2.

A global single-sheeted double many-body expansion potential energy surface is reported for the ground electronic state of ClO2. The potential energy surface is obtained by fitting 3200 energy points that map all atom-diatom dissociation channels as well as all relevant stationary points, including the well-known OClO and ClOO structures. The ab initio calculations are obtained at the multireference configuration interaction level of theory, employing the cc-pVXZ (X = D, T) Dunning basis sets, and then extrapolated to the complete basis set limit with the generalized uniform singlet- and triplet-pair protocol. The topographical features of the novel global potential energy surface are examined in detail.

Improvements in DFT Calculations of Spin-Spin Coupling Constants.

Different types of spin-spin coupling constants (SSCCs) for several representative small molecules are evaluated and analyzed using a combination of 10 exchange functionals with 12 correlation functionals. For comparison, calculations performed using MCSCF, SOPPA, other common DFT methods, and also experimental data are considered. A detailed study of the percentage of Hartree-Fock exchange energy in SSCCs and in its four contributions is carried out. From the above analysis, a combined functional formed with local Slater (34%), Hartree-Fock exchange (66%), and P86 correlation functional (S66P86) is proposed in this paper. The accuracy of the values obtained with this hybrid functional (mean absolute deviation of 4.5 Hz) is similar to that of the SOPPA method (mean absolute deviation of 4.6 Hz).

Computational NMR coupling constants: shifting and scaling factors for evaluating 1JCH.

Optimized shifting and/or scaling factors for calculating one-bond carbon-hydrogen spin-spin coupling constants have been determined for 35 combinations of representative functionals (PBE, B3LYP, B3P86, B97-2 and M06-L) and basis sets (TZVP, HIII-su3, EPR-III, aug-cc-pVTZ-J, ccJ-pVDZ, ccJ-pVTZ, ccJ-pVQZ, pcJ-2 and pcJ-3) using 68 organic molecular systems with 88 (1)JCH couplings including different types of hybridized carbon atoms. Density functional theory assessment for the determination of (1)JCH coupling constants is examined, comparing the computed and experimental values. The use of shifting constants for obtaining the calculated coupling improves substantially the results, and most models become qualitatively similar. Thus, for the whole set of couplings and for all approaches excluding those using the M06 functional, the root-mean-square deviations lie between 4.7 and 16.4 Hz and are reduced to 4-6.5 Hz when shifting constants are considered. Alternatively, when a specific rovibrational contribution of 5 Hz is subtracted from the experimental values, good results are obtained with PBE, B3P86 and B97-2 functionals in combination with HIII-su3, aug-cc-pVTZ-J and pcJ-2 basis sets.

A mathematical model applied for assisting the estimation of PMI in a case of forensic importance. First record of Conicera similis (Diptera: Phoridae) in a corpse.

We present a forensic case associated with skeletonized human remains found inside a cistern in a coastal town located in the eastern Iberian Peninsula (Valencian Regional Government, Spain). In order to analyse the particular environmental conditions that occurred during oviposition and development of the collected insects, estimated temperatures at the crime scene were calculated by a predictive mathematical model. This model analyses the correlation between the variability of the internal temperature depending on the variability of the external ones. The amplitude of the temperature oscillations inside the tank and the containment of the enclosure is reduced by the presence of water. Such variation occurred within about 2h due to the time required for heat exchange. The differential equations employed to model differences between outdoor and indoor temperatures were an essential tool which let us estimate the post-mortem interval (PMI) that was carried out by the study of the insect succession and the development time of the collected Diptera specimens under the adjusted temperatures. The presence of live larvae and pupae of Sarcophagidae and empty pupae of Calliphoridae, Sarcophagidae, Fanniidae, Muscidae, Phoridae and Piophilidae and the decomposition stage suggested the possibility that the remains were in the tank at least a year. We highlight the absence of Calliphora and Lucilia spp., and the first occurrence of the phorid Conicera similis in a human cadaver among the entomological evidence.

Ultrathin carbon nanotube with single, double, and triple bonds.

A metastable carbon nanotube with single, double, and triple bonds has been predicted from ab initio simulation. It results from the relaxation of an ideal carbon nanotube with chirality (2,1), without any potential barrier between the ideal nanotube and the new structure. Ten-membered carbon rings are formed by breaking carbon bonds between adjacent hexagons; eight-membered rings, already present in the ideal structure, become the smallest rings. This structure is stable in molecular dynamics simulations at temperatures up to 1000 K. Raman, infrared, and optical absorption spectra are simulated to allow its identification in the laboratory. The structure can be described as a double helical chain with alternating single, double, and triple bonds, where the chains are bridged by single bonds.

Electronic excitations of C60 aggregates.

Excitation properties of the isolated C(60) and (C(60))(N) model clusters (N = 2, 3, 4, 6 and 13) are studied using an a priori parameterized and self-consistent Hamiltonian, the Complete Neglect of Differential Overlap considering the l azimuthal quantum number method. This method properly describes electron excitations of the isolated C(60) after the configuration interaction of singles (CIS) procedure, when those are compared with experimental data in n-hexane solution and in a molecular beam. Geometry models of (C(60))(N) clusters to model the effect of aggregation were obtained from the fullerene fcc crystal. Some peaks in the low energy edge of the absorption spectrum appear corresponding to clustering effects, as well as small increases of bandwidths in the strong bands at the UV region. An analysis of the theoretical absorption spectrum for dimer models has been carried out, taking into account the influence of the distance between fullerene centers. The density of states of CIS for fullerene clusters in the range from 2.0 to 6.5 eV shows the possibility of electron transitions as functions of the size of the clusters.

Communication: Accurate determination of side-chain torsion angle χ1 in proteins: phenylalanine residues.

Quantitative side-chain torsion angle χ(1) determinations of phenylalanine residues in Desulfovibrio vulgaris flavodoxin are carried out using exclusively the correlation between the experimental vicinal coupling constants and theoretically determined Karplus equations. Karplus coefficients for nine vicinal coupling related with the torsion angle χ(1) were calculated using the B3LYP functional and basis sets of different size. Optimized χ(1) angles are in outstanding agreement with those previously reported by employing x ray and NMR measurements.

Approximating correlation effects in multiconfigurational self-consistent field calculations of spin-spin coupling constants.

The multiconfigurational self-consistent field (MCSCF) method in their approximations restricted and complete active spaces (RAS and CAS) provides a theoretically accurate description of the coupling constants of a wide range of molecules. To obtain accurate results, however, very large basis sets and large configuration spaces must be used. Nuclear magnetic resonance coupling constants for the equilibrium geometry have been calculated for a series of small molecules using approximated correlation contributions. The four contributions to the coupling constants (Fermi contact, spin dipolar, orbital paramagnetic, and orbital diamagnetic) have been calculated at the CAS and RAS MCSCF and second-order polarization propagator approximation levels using a large basis set. An additive model that considers the effect on the coupling constants from excitation of more than two electrons and from core-electron correlation is used to estimate the coupling constants. Compared with the experimental couplings, the best calculated values, which correspond to the MCSCF results, present a mean absolute error of 3.6 Hz and a maximum absolute deviation of 13.4 Hz. A detailed analysis of the different contributions and of the effects of the additive contributions on the coupling constants is carried out.

Karplus Equation for (3)JHH Spin-Spin Couplings with Unusual (3)J(180°) < (3)J(0°) Relationship.

Vicinal (3)JHH coupling constants for monosubstituted ethane molecules present the unusual relationship (3)JHH (180°) < (3)JHH (0°) when the substituent contains bonding and antibonding orbitals with strong hyperconjugative interactions involving bond and antibond orbitals of the ethane fragment. This anomalous behavior is studied as a function of the substituent rotation for three model systems (propanal, thiopropanal, and 1-butene) at the B3LYP/TZVP level. The consistency of this level of theory to study this problem is previously established using different ab initio methods and larger basis sets. The origin of the unusual (3)JHH(180°) - (3)JHH(0°) relationship is attributed to simultaneous σ/π hyperconjugative interactions σCα-Hα → π*Cc═X, and σCα-Cß â†’ π*Cc═X. These interactions depend on the substituent rotation and their effects are different for (3)JHH(180°) than for (3)JHH(0°). The modelization carried out shows an increase of those effects as the substituent changes from weaker (CH═CH2) to stronger (CH═S) electron acceptor π*C═X.

Molecular structure of chloro-dodecafluorosubphthalocyanato boron(III) by gas-phase electron diffraction and quantum chemical calculations.

The molecular structure of the chloro-dodecafluorosubphthalocyaninato boron(III) (F-SubPc) was determined with use of Gas Electron Diffraction (GED) and high-level quantum chemical calculations. The present results show that the F-SubPc molecule has a cone-shaped configuration, isoindole units are not planar, and the pyrrole ring has an envelope conformation. The structure parameters in the gas phase are determined. Some structural details can be observed such as the dihedral angle about the bond connecting the pyrrole ring and the benzene ring being ca. 174 degrees . High-level theoretical calculations with several extended basis sets for this molecule have been carried out. The calculations are in very good agreement with experimental methods: X-ray and GED. Nevertheless, some disagreements particularly related to the B-Cl bond distance found in GED are discussed. Vibrational frequencies were computed obtaining eight values below 100 cm-1 and three bending potentials were examined. They suggest that this molecule is very flexible.

Density functional theory predictions of isotropic hyperfine coupling constants.

The reliability of density functional theory (DFT) in the determination of the isotropic hyperfine coupling constants (hfccs) of the ground electronic states of organic and inorganic radicals is examined. Predictions using several DFT methods and 6-31G, TZVP, EPR-III and cc-pVQZ basis sets are made and compared to experimental values. The set of 75 radicals here studied was selected using a wide range of criteria. The systems studied are neutral, cationic, anionic; doublet, triplet, quartet; localized, and conjugated radicals, containing 1H, 9Be, 11B, 13C, 14N, 17O, 19F, 23Na, 25Mg, 27Al, 29Si, 31P, 33S, and 35Cl nuclei. The considered radicals provide 241 theoretical hfcc values, which are compared with 174 available experimental ones. The geometries of the studied systems are obtained by theoretical optimization using the same functional and basis set with which the hfccs were calculated. Regression analysis is used as a basic and appropriate methodology for this kind of comparative study. From this analysis, we conclude that DFT predictions of the hfccs are reliable for B3LYP/TZVP and B3LYP/EPR-III combinations. Both functional/basis set scheme are the more useful theoretical tools for predicting hfccs if compared to other much more expensive methods.

Theoretical isotropic hyperfine coupling constants of third-row nuclei (29Si, 31P, and 33S).

In a previous paper (Hermosilla, L.; Calle, P.; Garcia de la Vega, J. M.; Sieiro, C. J. Phys. Chem. A 2005, 109, 1114), an adequate computational protocol for the calculation of isotropic hyperfine coupling constants (hfcc's) was proposed. The main conclusion concerns the reliability of the scheme B3LYP/TZVP//B3LYP/6-31G* in the predictions of hfcc's with low computational cost. In the present study, we gain insight into the behavior of the above functional/basis set scheme on nuclei of the third row, for which few systematic studies have been carried out up to the present date. The systems studied are neutral, cationic, anionic, localized, and conjugated radicals, containing (29)Si, (31)P, and (33)S nuclei. After carrying out a regression analysis, we conclude that density functional theory (DFT) predictions on the hfcc's of the third-row nuclei are reliable for B3LYP/TZVP by using an optimized geometry with B3LYP/6-31G* combination. By comparison with other much more computationally demanding schemes, namely, B3LYP/cc-pVTZ and B3LYP/cc-pVQZ, we conclude that the B3LYP functional in conjunction with the TZVP basis set is the most useful computational protocol for the assignment of experimental hfcc's, not only for nuclei of first and second rows, but also for those of the third row.

Polarized basis sets of Slater-type orbitals: H to Ne atoms.

We present three Slater-type atomic orbital (STO) valence basis (VB) sets for the first and second row atoms, referred to as the VB1, VB2, and VB3 bases. The smallest VB1 basis has the following structure: [3, 1] for the H and He atoms, [5, 1] for Li and Be, and [5, 3, 1] for the B to Ne series. For the VB2 and VB3 bases, both the number of shells and the number of functions per shell are successively increased by one with respect to VB1. With the exception of the H and Li atoms, the exponents for the VB1 bases were obtained by minimizing the sum of the Hartree-Fock (HF) and frozen-core singles and doubles configuration interaction (CISD FC) energies of the respective atoms in their ground state. For H and Li, we minimized the sum of the HF and CISD FC energies of the corresponding diatoms (i.e., of H(2) or Li(2)) plus the ground-state energy of the atom. In the case of the VB2 basis sets, the sum that was minimized also included the energies of the positive and negative ions, and for the VB3 bases, the energies of a few lowest lying excited states of the atom. To account for the core correlations, the VBx (x = 1, 2, and 3) basis sets for the Li to Ne series were enlarged by one function per shell. The exponents of these extended (core-valence, CV) basis sets, referred to, respectively, as the CVBx (x = 1, 2, and 3) bases, were optimized by relying on the same criteria as in the case of the VBx (x = 1, 2, and 3) bases, except that the full CISD rather than CISD FC energies were employed. We show that these polarized STO basis sets provide good HF and CI energies for the ground and excited states of the atoms considered, as well as for the corresponding ions.

A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins.

Nonplanar saddled (sad) ruffled (ruf) and domed (dom) conformations of the Mg-porphyrin (MgP) macrocycle in several degrees of deformation have been computed. These symmetrical distortion modes were induced in unsubstituted macrocycle using molecular definitions for calculations which permits us to achieve a systematical variation of the nonplanarity varying only a convenient geometrical parameter of the molecule. Series of nonplanar macrocycles like those synthesized in previous works employing peripheral substitutions are obtained. The procedure here used to induce deformations gives the possibility of investigating the modulator role of the out-of-plane distortions on the geometry and electronic properties of the porphyrin avoiding additional influences due to the substituents or the surrounding protein scaffolding.

A minimal multiconfigurational technique.

A direct minimization method previously presented by the authors is applied here to biconfigurational wave functions. A very moderate increasing in the time by iteration with respect to the one-determinant calculation and good convergence properties have been found. So qualitatively correct studies on singlet systems with strong biradical character can be performed with a cost similar to that required by Hartree-Fock calculations.