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.

Management of interruptions to fractionated radiotherapy treatments: Four and a half years of experience.

BACKGROUND AND PURPOSE: The study objective was to report our four-and-a half years experience (March 1 2011-August 15 2015) of a program to manage interruptions in fractionated radiotherapy treatments. METHODS: A program was developed, based on a specific database, to manage treatment interruptions. Benefits of the program were analyzed in reference to previously published data. Analysis was also performed of two measures to reduce OTT prolongation and improve treatment outcomes: working on public holidays and conducting treatment unit maintenance on Saturdays. RESULTS: The study included 2352 patients. Patients with head and neck cancer obtained the greatest benefit from the program, with a mean increase in TCP of 3.5% and a benefit of at least 4% in 45.6% of them. In prostate cancer patients, the likelihood of biochemical failure was reduced by a mean of 2.0% and was reduced by at least 4% in 19.7% of them. Application of the two proposed measures would have improved the TCP by a mean of 5.4% in head and neck cancer patients. The impact of the compensations program and proposed measures is lesser in the remaining cancer types studied. CONCLUSIONS: Implementation of a compensation program has a significant impact on patients with head and neck or prostate cancer but OTT prolongation remains excessive in many treatments. The introduction of fractions on public holidays would assist in the meeting of recommendations for these patients.

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.

A method to relate StarTrack(®) measurements to R50 variations in clinical linacs.

The relation between the data recorded with any device for the daily checking of the behavior of a clinical linac and the reference magnitudes to be monitored may be unknown. An experimental method relating the energy stability of the electron beam measured with StarTrack(®) to the R50 beam quality index is proposed. The bending magnet current is varied producing a change in the exit energy window and, therefore, a modification of the R50 value. For different values of this current, the output data of StarTrack(®) and the R50, obtained from depth doses measured in a water phantom are determined. A linear fit between both sets of data allows the identification of the StarTrack(®) output that provides the best way to obtain the quality index R50, for each beam nominal energy. Using these fits, an historical datum series is used to analyze the method proposed in the daily quality control. The ouput data of the StarTrack(®) and the R50 values show a good linear correlation. It is possible to establish a methodology that allows the monitoring of R50 by direct use of the daily quality control data measured with StarTrack(®). A method to monitor R50 in the daily quality control using the StarTrack(®) device has been developed. The method may be applied to similar devices in which the statistical control variable does not show a linear behavior with R50.

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.

Quality control for system count rate performance with scatter in gamma cameras.

We aimed to analyze the optimal conditions to carry out the periodical statistical control tests of the gamma camera count rate performance. First we focused in reproducing the actual R(20) value of the gamma camera response. Second we studied the variability of this parameter in the statistical control test. We performed a reference measurement, which consisted of the determination of the complete curve relating observed and incident count rates, the counting model describing it and the reference R(20). This reference determined the conditions for the statistical control tests and the way to analyze the results obtained. Results from three different gamma cameras were studied. Each gamma camera showed a different behavior and required specific data analysis. The optimal conditions to perform the statistical control test were determined in each case. Our procedure provides the information necessary to correlate the average value of R(20) obtained in the quality control test with the reference one. The critical requirement to perform any statistical control test, that is to have a reduced variability of the control variable, can be fulfilled in this case only for relatively high activities.

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.

On the molecular electron structure of three phosphinine-containing macrocycles.

A broad set of structural models and theoretical methods has been successfully used for studying both the molecular electron structure of the silacalix[3]phosphinine and the changes of the macrocycle core under the conditions that frequently correspond to its complexes with metals. The macrocycle core of the silacalix[3]phosphinine and its neutral derivatives are strongly deviated from the main molecular plane. The phosphorous electron lone pairs and the pi-cloud of the phosphinine units give the main contribution to the electron valence structure in the silacalix[3]phosphinine and also in its both oxidized and reduced derivatives. Although the electron lone pairs of the P atoms tend to be strongly repulsive, they are either totally or partially extended above all the fragment of the phosphorous atoms depending on geometrical factors or even strongly coupled with the pi-cloud of the phosphinine units. Electronic processes that take away part of the electron density from the macrocyle favor both its planar configuration and the asymmetric distribution of the valence electrons in the silacalix[3]phosphinine and its derivatives. The limit condition to this effect is the appearance of a new in-plane sigma molecular orbital between the P atoms of two neighboring phosphinine units.

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.