Density functional theory study of 14N isotropic hyperfine coupling constants of organic radicals

Nitrogen hyperfine coupling constants (hfccs) of organic radicals have been calculated by density functional theory (DFT) methodology. The capability of the B3LYP functional, combined with 6-31G*, TZVP and EPR-III basis sets, to reproduce experimental nitrogen coupling constant data has been analyzed for 109 neutral, cationic and anionic radicals, all of them containing at least one nitrogen atom. The results indicate that the selection of the basis set plays an important role in the accuracy of DFT calculations of hfccs, mainly in relation with the composition of the primitive functions and the quantum number of those functions. The main conclusion obtained is the high reliability of the scheme B3LYP/6-31G* for the prediction of nitrogen hfccs with very low computational cost.     

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.     

DFT study of the EPR spectral pattern of propagating methacrylic radicals

The EPR spectral pattern observed in the bulk polymerization of methacrylic monomers was theoretically investigated by DFT methodology. The conformational analysis of the propagating radical by the rotation around the C–C_β bond, was performed using the B3LYP/6-31G^* computational scheme. To obtain accurate values of the isotropic hyperfine coupling constants (hfccs) a higher level protocol, B3LYP/TZVP//B3LYP/6-31G^*, was applied. The experimental 13-line spectrum registered at the first stage of the polymerization was assumed to correspond to a free rotating radical in a fluid medium and it was simulated just considering the most stable conformation. The 9-line spectrum registered at high conversions was interpreted in terms of highly hindered rotational conformers frozen in the very viscous medium. This spectrum was well reproduced by a model which considers the sum of the individual spectra of the conformations spread around the most probable. Each of these contributing spectra was obtained on the basis of the computed hfccs for the considered conformations and weighted by his relative Boltzmann population according to the DFT analysis. Besides, the calculated hfccs showed an excellent agreement with those predicted by the Heller–McConnell relationship, which confirms the coherence of the DFT methodology for this kind of calculations.     

Proton affinities of ketones, vicinal diketones and α-keto esters: a computational study

The proton affinities of seven different ketones, vicinal diketones, and α-keto esters (acetophenone, 2,2,2-trifluoroacetophenone, 2,3-butanedione, 1-phenyl-1,2-propanedione, methyl pyruvate, ethyl benzoylformate, and ketopantolactone) have been evaluated theoretically using the conventional ab initio HF and several post-HF methods (MP2, MP4, CCSD), density functional methods with the B3LYP hybrid functional, as well as some ab initio model chemistries [CBS-4M, G2(MP2), and G3(MP2)//B3LYP]. The chemical compounds studied are frequently used substrates in the asymmetric hydrogenation over chirally modified platinum catalysts where the protonation properties of the chiral modifier and the substrates are of great interest. In most cases, the proton affinities (PAs) evaluated with the CCSD/6-311+G(d,p)//B3LYP/TZVP and G2(MP2) methods are in good agreement with the existing experimental ones. However, the previously reported PA of 2,3-butanedione seems to be too high by 10-15 kJ mol⁻¹. The B3LYP/TZVP//B3LYP/TZVP and MP2/6-311+G(d,p)//B3LYP/TZVP model chemistries predict proton affinities that are systematically higher and lower than the experimental PAs, respectively. If proton affinities are evaluated as the average of the PAs calculated with these two theoretical methods a very good agreement with the experimental results is obtained. The mean absolute deviation (MAD) from experiment of this combination method for the PAs of 13 test molecules is 4.0 kJ mol⁻¹. For 9 molecules composed only of first-row atoms the MAD is 2.5 kJ mol⁻¹. The B3LYP/TZVP//B3LYP/TZVP and MP2/6-311+G(d,p)//B3LYP/TZVP methods provide significant savings in computational time and disk space compared to the CCSD/6-311+G(d,p)//B3LYP/TZVP and G2(MP2) models. Therefore, it is suggested that if no experimental or highly accurate theoretical data is available (due to computational cost), the proton affinities of similar compounds as investigated in this paper, can be evaluated with the combination method. For the studied molecules, this method gives the following PAs (in kJ mol⁻¹): 788 (2,3-butanedione, exptl 802); 798 (2,2,2-trifluoroacetophenone, exptl 799); 811 (ketopantolactone); 813 (methyl pyruvate); 825 (1-phenyl-1,2-propanedione); 862 (acetophenone, exptl 861); 865 (ethyl benzoylformate).     

Assessment of density functional theory methods for the computation of heats of formation and ionization potentials of systems containing third row transition metals

The performance of several different density functional theory (DFT) methods, including GGA, hybrid-GGA, meta-GGA, and hybrid-meta-GGA methods, have been assessed in terms of their ability to accurately compute both heats of formation and ionization potentials of systems containing third row transition metals. Two different basis sets were used in this study: 6-31G** and TZVP. It is found that the triple-zeta quality TZVP basis set generally produces the best results for both heats of formation and ionization potentials. One important observation made in this study is that the inclusion of exact exchange terms in DFT methods generally results in more consistently accurate results for both heats of formation and ionization potentials of transition metal systems. In general, DFT methods do not yield good ionization potential results for systems containing titanium or zinc. For heats of formation, it is found that the hybrid-meta-GGA functional, TPSS1KCIS, yields the best overall results when combined with the TZVP basis set, while PBE1PBE (hybrid-GGA) gives the best results for the 6-31G** basis. The hybrid-GGA functional, B3LYP, is found to produce the lowest overall errors for ionization potentials when combined with both 6-31G** and TZVP.     

Understanding selenocysteine through conformational analysis,proton affinities,acidities and bond dissociation energies

Density functional methods have been employed to characterize the gas phase conformations of selenocysteine. The 33 stable conformers of selenocysteine have been located on the potential energy surface using density functional B3LYP/6‐31+G* method. The conformers are analyzed in terms of intramolecular hydrogen bonding interactions. The proton affinity, gas phase acidities, and bond dissociation energies have also been evaluated for different reactive sites of selenocysteine for the five lowest energy conformers at B3LYP/6‐311++G*//B3LYP/6‐31+G* level. Evaluation of these intrinsic properties reflects the antioxidant activity of selenium in selenocysteine. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

已烯自由基阳离子的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-31G(d,p),6-31+G(d,p),6-311G(d,p)及6- 311+G(d,p)基组,分别对1-C_6H_(12)~+,2-C_6H_(12)~+和3-C_6H_(12)~+的各种构 象进行了几何构型优化,并在B3LYP/6-311G(d,p)水平上进行了频率分析计算,在 各优化构型上,使用B3LYP和MP2(full)方法进行了超精细结构的计算。计算的3- C_6H_(12)~+的超精细偶合常数比以往的计算结果更好;1-C_6H_(12)~+和2-C_6H_ (12)~+的超精细偶合常数目前尚无实验数据报道,本计算预言了它们的超精细偶合 常数和最稳定构型。     

Secondary orbital effect in the electrocyclic ring closure of 7-Azahepta-1,2,4,6-tetraeneA CASSCF molecular orbital study

Results of (10,9)CASSCF/6-31G* and B3LYP/6-31G* level calculations on the potential surface for the electrocyclic ring closure of E-7-azahepta-1,2,4,6-tetraene 3 to 1-aza-6-methylidenecyclohexa-2,4-diene ( 4) are reported, as well as parallel calculations on the electrocyclizations of hepta-1,2,4,6-tetraene 5, hexa-1,3,5-triene 7, Z and E-1-aza-1,3,5-hexatrienes 9 and 10, and Z-7-azahepta-1,2,4,6-tetraene 12 for purposes of careful comparison. The 3 --> 4 rearrangement has been studied computationally with density functional theory (DFT) by others, leading to disagreement over whether it is pseudopericyclic (de Lera, A. R.; Alvarez, R.; Lecea, B.; Torrado, A.; Cossío, F. P. Angew. Chem., Int. Ed. 2001, 40, 557-561; de Lera, A. R.; Cossío, F. P. Angew. Chem., Int. Ed. 2002, 41, 1150-1152) or pericyclic (Rodríguez-Otero, J.; Cabaleiro-Lago, E. Angew. Chem., Int. Ed. 2002, 41, 1147-1150). In accordance with disrotatory motion, the normal mode vectors for TS 3-->4 calculated at the (10,9)CASSCF/6-31G* level show a greater magnitude of rotation of the N1-H group relative to the N1-C2 bond being formed than in TS 3-->4 calculated at the B3LYP/6-31G* level. Furthermore, comparison of orbital correlation diagrams constructed entirely from localized complete active space (CAS) molecular orbitals (MOs) for the electrocyclizations of 3, 5, 7, 9, and 10 suggest that it is the highest occupied delocalized pi-MO of 3 that is primarily responsible for sigma-bond formation in 4, not the terminal allenyl pi-bond MO. However, there does appear to be a special secondary orbital effect role for the nitrogen lone-pair and hence the process is likely neither purely pericyclic nor pseudopericyclic.     

2,3,7,8-四氯苯并二英分子结构与热力学性质的理论研究

用密度泛函理论(DFT)和从头算(ab initio)方法,在B3LYP/6-31G、 B3LYP/6-31G*、 B3LYP/6-311G*和MP2/6-31G*水平上全优化计算了2,3,7,8-四氯苯并二英(2,3,7,8-TCDD)的几何构型、电子结构和振动频率,并用校正后的频率计算了298～1500 K的标准热力学函数,同时用半经验的PM3 SCF-MO进行了同样的计算,计算结果与实验值及文献值较好地吻合.     

A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: consequences for immunochemistry of penicillins

Herein, we present results of a computational study on benzylpenicillin attachment to Lys199 of human serum albumin via an aminolysis reaction. The internal geometry of the reactive part of the system was taken from previous work at the B3LYP/6-31+G* level on the water-assisted aminolysis reaction of a penicillin model compound (Díaz, N.; Suárez, D.; Sordo, T. L. J. Am. Chem. Soc. 2000, 122, 6710--6719). The protein environment around Lys199, the 6-acylamino side chain, and the 2-methyl groups of benzylpenicillin were relaxed by carrying out geometry optimizations with a hybrid QM/MM method (PM3/AMBER). Two different mechanistic routes were explored: a one-step water-assisted process and a carboxylate and water-assisted route in which the beta-lactam carboxylate and the ancillary water molecule mediate the proton transfer from the epsilon-amino group of Lys199 to the beta-lactam leaving N atom. The corresponding energy profiles in the protein combine the B3LYP/6-31+G* and PM3 energies of the reactive subsystem (benzylpenicillin + Lys199 side chain + the ancillary water molecule) and semiempirical PM3 energies of the entire system evaluated with a "divide and conquer" linear-scaling method. It is observed that penicillin haptenation to HSA can proceed through the water-assisted concerted mechanism which is calculated to have a high energy barrier of approximately 38 kcal/mol, in agreement with the experimentally observed slow reaction kinetics.     

Density functional theory calculations of the lowest energy quintet and triplet states of model hemes: role of functional, basis set, and zero-point energy corrections

We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results insignificantly for iron(II) porphyrin coordinated with imidazole. Poor performance of a "locally dense" basis set with a large number of basis functions on the Fe center was observed in calculation of quintet-triplet gaps. Our results lead to a series of suggestions for density functional theory calculations of quintet-triplet energy gaps in ferrohemes with a single axial imidazole; these suggestions are potentially applicable for other transition-metal complexes.     

四唑互变异构反应的密度泛函理论(DFT)研究

运用11种密度泛函理论方法对四唑互变异构反应进行了计算研究。结果表明,B3LYP-DFT法与从头算的优化几何和能量最为吻合;在6-31^*基组下B3LYP计算的IR频率与MP2/6-311G^*^*计算结果相差很小;用未经校正的B3LYP计算频率求得的产物(2H-四唑)的热力学性质与实测结果也完全一致;由此推荐B3LYP-DFT法适合于对四唑化合物作系统研究。     

Investigation of the use of B3LYP zero-point energies and geometries in the calculation of enthalpies of formation

The use of B3LYP/6–31G^* zero-point energies and geometries in the calculation of enthalpies of formation has been investigated for the enlarged G2 test set of 148 molecules [J. Chem. Phys. 106 (1997) 1063]. A scale factor of 0.96 for the B3LYP zero-point energies gives an average absolute deviation nearly the same as scaled HF/6–31G^* zero-point energies for G2, G2(MP2), and B3LYP/6–311 + G(3df,2p) enthalpies. A scale factor of 0.98, which has been recommended in some studies, increases the average absolute deviation by about 0.2 kcal/mol. Geometries from B3LYP/6–31G^* are found to do as well as MP2/6–31G^* geometries in the calculation of the enthalpies of formation.     

吲哚分子振动光谱的密度泛函理论研究

用多种密度泛函理论(DFT)方法(BLYP/6-31G^*^*,B3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)对吲哚分子的平衡几何构型进行了优化。在优化构型的基础上计算了吲哚分子的谐力场、振动基频和红外光谱强度。计算得到的振动频率与实验值比较平均偏差对四种计算方法(BLYP/6-31G^*^*,P3LYP/6-31G^*^*,B3PW91/6-31G^*^*和SVWN/6-31G^*^*)分别为16.3,40.5,45.1和26.4cm^-^1。BLYP/6-31G^*^*理论力场被用于吲哚分子的简正坐标分析计算中。根据振动率的势能分布(PEDs)对此分子的振动基频进行了理论归属。     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。     

The O-H stretching mode of a prototypical photoacid as a local dielectric probe

We investigate the OH stretch vibrational frequency shifts of a prototype photoacid, 2-naphthol (2N), when dissolved in solvents of low polarity. We combine femtosecond mid-infrared spectroscopy and a theoretical model based on the Pullin-van der Zwan-Hynes perturbative approach to explore vibrational solvatochromic effects in the ground S(0) and the first electronically excited (1)L(b) states. The model is parametrized using density functional theory (DFT), at the B3LYP/TZVP and TD-B3LYP/TZVP levels for the 2N chromophore in the S(0) and (1)L(b) states, respectively. From the agreement between experiment and theory we conclude that vibrational solvatochromic effects are dominated by the instantaneous dielectric response of the solvent, while time-dependent nuclear rearrangements are of secondary importance.     

Single-site mutation and secondary structure stability: an isodesmic reaction approach. The case of unnatural amino acid mutagenesis Ala-->Lac

A method is described to evaluate backbone interactions in proteins via computational unnatural amino acid mutagenesis. Several N-acetyl polyalanyl amides (AcA(n)NH(2)) were optimized in the representative helical (3(10)-, 4(13)-, and a "hybrid" kappa-helix, n = 7, 9, 10, 14) and hairpin (two- and three-stranded antiparallel beta-sheets with type I turns betaalphaalphaepsilon, n = 6, 9, 10) conformations, and extended conformers of N-acetyl polyalanyl methylamides (n = 2, 3) were used to derive multistranded beta-sheet fragments. Subsequently, each residue of every model structure was substituted, one at a time, with l-lactic acid. The resulting mutant structures were again optimized, and group-transfer energies DeltaE(GT) were obtained as heats of the isodesmic reactions: AcA(n)NHR + AcOMe --> AcA(x)LacA(y)NHR + AcNHMe (R = H, CH(3)). These group-transfer energies correlate with the degree of charge polarization of the substituted peptide linkages as measured by the difference Deltae in H and O Mulliken populations in HN-C=O and with the H-bond distances in the "wild-type" structures. A good correlation obtains for the HF/3-21G and B3LYP/6-31G* group-transfer energies. The destabilization effects are interpreted in terms of loss of interstrand and intrastrand H-bonds, decrease in Lewis basicity of the C=O group, and O...O repulsion. On the basis of several comparisons of Ala --> Lac DeltaE(GT)'s with heats of the NH --> CH(2) substitutions, the latter contribution is estimated (B3LYP/6-31G*) to range between 1.5 and 2.4 kcal mol(-1), a figure close to the recent experimental DeltaDeltaG(o) value of 2.6 kcal mol(-1) (McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am.Chem. Soc. 2003, 125, 9314). The partitioning yields the following maximum values of the electronic association energy of H-bonds in the examined sample of model structures (B3LYP/6-31G* estimates): 3(10)-helix D(e) = -1.7 kcal mol(-1), alpha-helix D(e) = -3.8 kcal mol(-1), beta-sheet D(e) = -6.1 kcal mol(-1). The premise of experimental evaluations of the backbone-backbone H-bonding that Ala --> Lac substitution in proteins is isosteric (e.g., Koh, J. T.; Cornish, V. W.; Schultz, P. G. Biochemistry 1997, 36, 11314) is often but not always corroborated. Examination of the integrity of H-bonding pattern and phi(i), psi(i) distribution identified several mutants with significant distortions of the "wild-type" structure resulting inter alia from the transitions between i, i + 3 and i, i + 4 H-bonding in helices, observed previously in the crystallographic studies of depsipeptides (Ohyama, T.; Oku, H.; Hiroki, A.; Maekawa, Y.; Yoshida, M.; Katakai, R. Biopolymers 2000, 54, 375; Karle, I. L.; Das, C.; Balaram, P. Biopolymers 2001, 59, 276). Thus, the isodesmic reaction approach provides a simple way to gauge how conformation of the polypeptide chain and dimensions of the H-bonding network affect the strength of backbone-backbone C=O...HN bonds. The results indicate that the stabilization provided by such interactions increases on going from 3(10)-helix to alpha-helix to beta-sheet.     

CF3 rotation in 3-(trifluoromethyl)phenanthrene. X-ray diffraction and ab initio electronic structure calculations

The molecular and crystal structure of 3-(trifluoromethyl)phenanthrene has been determined by X-ray diffraction. The structure of the isolated molecule has been calculated using electronic structure methods at the HF/3-21G, HF/6-31G, MP2/6-31G and B3LYP/6-31G levels. The potential energy surfaces for the rotation of the CF3 group in both the isolated molecule and cluster models for the crystal were computed using electronic structure methods. The barrier height for CF3 rotation in the isolated molecule was calculated to be 0.40 kcal mol(-1) at B3LYP/6-311+G//B3LYP/6-311+G. The B3LYP/6-31G calculated CF3 rotational barrier in a 13-molecule cluster based on the X-ray data was found to be 2.6 kcal mol(-1). The latter is in excellent agreement with experimental results from the NMR relaxation experiments reported in the companion paper (Beckmann, P. A.; Rosenberg, J.; Nordstrom, K.; Mallory, C. W.; Mallory, F. B. J. Phys. Chem. A 2006, 110, 3947). The computational results on the models for the solid state suggest that the intermolecular interaction between nearest neighbor pairs of CF3 groups in the crystal accounts for roughly 75% of the barrier to rotation in the solid state. This pair is found to undergo cooperative reorientation. We attribute the CF3 reorientational disorder in the crystal as observed by X-ray diffraction to the presence of a pair of minima on the potential energy surface and the effects of librational motion.     

线型碳链PC2nP的结构和电子光谱的密度泛函理论研究

应用密度泛函理论,在B3LYP/6-31G**和B3LYP/6-311G**水平上优化得到了线型簇合物PC2nP(n=1-10)的基态平衡几何构型,计算了它们的谐振动频率.在基态平衡构型下,利用含时密度泛函理论,计算得到了簇合物PC2nP(n=1-10)的垂直激发能和相应的振子强度,导出了激发能与体系大小n的解析关系式.