Inductive effects in radicals calculated from DFT energies; substituted bicyclo[2.2.2]octan-1-yloxy radicals

Energies of a series of 4-substituted 1-oxybicyclo[2.2.2]octan-1-yloxy radicals with 18 various substituents were calculated within the framework of the DFT theory at the levels UB3LYP/6-311+G(d,p)//UB3LYP/6-311+G(d,p) and UB3LYP/6-311++G(2df,p)//UB3LYP/6-311+G(d,p) and compared with similar series of the parent alcohols, their deprotonated and protonated forms calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and B3LYP/6-311++G(2df,p)//B3LYP/6-311+G(d,p). The two levels are of the same performance and both are sufficient for molecules of this type according to comparison with scarce experimental gas-phase acidities and basicities. The substituent effects were analyzed in terms of isodesmic equations. In addition to strong dependence on the substituent inductive effect, a slight dependence on the electronegativity of the first atom of the substituent was proven in certain cases. In all aspects, there is no qualitative difference between the effects on radicals and on similar closed shell species. Radicals behave as slightly electron deficient; the substituent effect is weaker than that on the ions but stronger than on neutral molecules.     

Substituent effects on the acidity of weak acids. 1. Bicyclo[2.2.2]octane-1-carboxylic acids and bicyclo[1.1.1]pentane-1-carboxylic acids

The acidities of 3- and 4-substituted bicyclooctane-1-carboxylic acids and 3-substituted bicyclo[1.1.1]pentane-1-carboxylic acids have been calculated at the MP2/6-311++G** theoretical level. There is good agreement between the calculated and observed gas-phase acidities. The acidities of the 4-substituted bicyclooctane acids were found to be linearly dependent on the C-X bond dipoles, as expected from a field effect. The substituents had a negligible effect on the electron density at C1. The difference in acidity between 4-chlorobicyclo[2.2.2]octane-1-carboxylic acid and the parent acid (6.2 kcal/mol) is reproduced by the Kirkwood-Westheimer treatment of substituent effects on acidity, but only if the bicyclooctane ring is given an effective dielectric constant of unity. The acidities of the 3-substituted bicyclooctane acids are linearly related to the corresponding 4-substituted acids with a slope of 0.9. The acidities of the 3-substituted bicyclo[1.1.1]pentane-1-carboxylic acids are linearly related to the C-X bond dipoles for this ring system (which are different than those for the bicyclooctanes), and they are also linearly related to the acidity of the 4-substituted bicyclo[2.2.2]octanecarboxylic acids with a slope of 1.34. The larger slope is due to the smaller bridgehead-bridgehead distance in the bicyclopentane ring than in bicyclo[2.2.2]octane.     

Inductive effects in isolated molecules: 4-substituted bicyclo[2.2.2]octane-1-carboxylic acids

Energies of sixteen 4-substituted bicyclo[2.2.2]octane-1-carboxylic acids, their anions, and pertinent 1-substituted bicyclo[2.2.2]octanes were calculated within the framework of density functional theory at the B3LYP/6-311 + G(d,p) level. Substituent effects were evaluated separately in the acid molecule and in the anion in terms of isodesmic homodesmotic reactions. In both cases, the substituent effects are proportional and of opposite sense, that in the anion being eight times greater; in the effect on acidity they are summed. The calculated acidities are in agreement with experimental values with a standard deviation of 1.1 kJ mol-1, and are recommended as a model for evaluating the inductive effect of various substituents, whether they are experimentally accessible or not. The resulting values are closely related to other scales but can be determined more reliably, particularly when compared with the previous quantum chemical method. We also checked electrostatic calculations and confirmed their very approximate character, particularly in the case of unsymmetrical substituents or of substituents with zero dipole moment.     

Substituent effects on the acidity of weak acids. 3. Phenols and benzyl alcohols

The gas-phase acidities of meta- and para-substituted phenols have been calculated at the B3LYP/6-311+G, MP2/6-311+G, MP2/6-311++G, and MP2/6-311+G(2df,2pd) theoretical levels. The larger basis sets give the more satisfactory DeltaHacid values that are correlated with the observed acidities with a slope close to unity. They are systematically about 2 kcal/mol too small. The acidities of most substituted phenols are linearly related to those of the corresponding substituted benzoic acids and benzyl alcohols. Here, the substituent effect is a Coulombic interaction (field effect) of the distributed charge in the benzene ring with the negative charge of the anionic center. The exceptions are strong para-substituted pi-acceptors such as NO(2) and CHO, and to a smaller extent, CN and CF(3). Here there is direct charge transfer from the phenoxide oxygen to the substituent.     

Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids

Energies of 20 alkyl-substituted benzoic acids were calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p)//MP2/6-311+G(d,p); the pertinent enthalpies at 298 K were calculated at the same levels. Comparison with experimental enthalpies of formation Delta(f)H degrees (g)(298) was carried out in terms of isodesmic reactions, that is, in the relative values. Of the four calculated quantities, the DFT enthalpies yielded best correlation with the standard deviation of 2.1 kJ mol(-1), near to the experimental uncertainty; the DFT energies are only slightly worse and the MP2 enthalpies or energies much worse. However, the DFT method overestimated systematically the substituent effects and had to be calibrated. Comparison with the experimental gas-phase acidities was less telling and the fit was worse because both methods overestimated the substituent effects. Extending the base in selected examples did not give better results. Although the systematic deviations are evidently due to the imperfections of the theoretical models, individual big deviations should be attributed to experimental errors or to the abnormal behavior of certain compounds at the experimental conditions. From this point of view, three examples of the so-called long-range effect claimed in the case of different benzoic acid derivatives, always for substituents in the meta position, must be refused as unproven because the experimental energies were not confirmed by calculations.     

Energetics of oxaspirocycle prototypes: 1,7-dioxaspiro[5.5]undecane and 1,7,9-trioxadispiro[5.1.5.3]hexadecane

The relative gas-phase energetics of several low-lying isomers of 1,7-dioxaspiro[5.5]undecane and 1,7,9-trioxadispiro[5.1.5.3]hexadecane have been calculated with second-order Mller-Plesset perturbation theory and basis sets as large as aug-cc-pVQZ. Relative energies in THF, dichloromethane, acetone, and DMSO have been estimated with corrections from polarized continuum model calculations at the B3LYP/6-311+G(d) level. In the most stable conformation of 1,7-dioxaspiro[5.5]undecane, both rings adopt chair conformations, and both oxygens are axially disposed (2A). It is more than 2 kcal mol(-1) more stable than all the other conformers. In agreement with previous work, the "twist-boat" trans isomer (3A) is the most stable isomer of 1,7,9-trioxadispiro[5.1.5.3]hexadecane. However, in contrast to this earlier study, an "all-chair" conformation (3B) is found to be the most stable cis isomer of 1,7,9-trioxadispiro[5.1.5.3]hexadecane (E approximately 0.5 kcal mol(-1) in acetone and DMSO). Gauge-independent atomic orbital computations at the B3LYP/6-311+G(d) level indicate that this is the only cis isomer with (13)C NMR chemical shifts that are qualitatively consistent with the experimental spectra.     

A theoretical rationalization of the asymmetric induction in sulfinyl-directed [5C + 2C] intramolecular cycloadditions

A computational DFT examination (B3LYP/6-31G and B3LYP/6-311+G//B3LYP/6-31G) of the thermal [5C + 2C] cycloaddditions of 6-acetoxy-3-pyranones and 3-silyloxy-4-pyrones with tethered alkenyl sulfoxides confirms that the high level of diastereofacial selectivity obtained is ultimately due to the preference of the alkenesulfinyl group to adopt a well-defined conformation in the transition state of the reaction. This conformation, which is different from that found in the ground state, is most probably dictated by dipolar interaction effects between the sulfoxide and the oxidopyrylium ylide intermediate.     

[GeCN2]分子异构化势能面的理论研究

在CCSD(T)/6-311＋G(2df)//B3LYP/6-311＋G(d)水平下, 研究了四原子分子 [GeCN2]的各个异构体的几何结构、红外振动光谱、相对能量及异构化和解离稳定性, 构建了[GeCN2]势能面. 我们得到了7个[GeCN2]异构体, 包括5个直线型结构GeNCN (1), GeNNC (2), NGeCN (3), NGeNC (4), GeCNN (5)和2个环形结构Ge-cCNN (6)和Ge-cNCN (7). 其中异构体5, 6, 7是我们新找到的构型, 而且GeCNN (5)是整个势能面上稳定性仅次于GeNCN (1)的异构体. 几何和电子结构分析表明, GeCNN (5)具有共轭三键结构: Ge≡C—N≡N:. 由于具有良好的热力学和动力学稳定性, 异构体GeCNN (5)有望在实验中观测到. 我们建议利用过渡金属羰基化合物的络合作用可以进一步稳定GeCNN (5). 本研究为寻找新型含高周期元素的多重键化合物提供了理论线索.     

Carbon-to-carbon identity proton transfer from allene, ketene, ketenimine, and thioketene to their respective conjugate anions in the gas phase. An ab initio study.

Gas-phase acidities of CH2=C=X (X = CH2, NH, O, and S) and barriers for the identity proton transfers (X=C=CH2 + HC triple bond C-X- right harpoon over left harpoon -X-C triple bond CH + CH2=C=X) as well as geometries and charge distributions of CH2=C=X, HC triple bond C-X- and the transition states of the proton transfer were determined by ab initio methods at the MP2/6-311+G(d,p)//MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. The acidities were also calculated at the CCSD(T)/6-311+G(2df,p) level. A major objective of this study was to examine how the enhanced unsaturation of CH2=C=X compared to that of CH3CH=X may affect acidities, transition state imbalances, and intrinsic barriers of the identity proton transfer. The results show that the acidities are all higher while the barriers are lower than for the corresponding CH3CH=X series. The transition states are all imbalanced but less so than for the reactions of CH3CH=X.     

NMR spectra, GIAO and charge density calculations of five-membered aromatic heterocycles

The B3LYP/6-31+G(d) molecular geometry optimized structures of 17 five-membered heterocycles were employed together with the gauge including atomic orbitals (GIAO) density functional theory (DFT) method at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants. The method of geometry optimization for pyrrole (1), N-methylpyrrole (2) and thiophene (7) using the larger 6-311++G(d,p) basis sets at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,p) and B3LYP/cc-pVTZ levels of theory gave little difference between calculated and experimental values of coupling constants. In general, the (1)H and 13C chemical shifts for all compounds are in good agreement with theoretical calculations using the smaller 6-31 basis set. The values of nJHH(n=3, 4, 5) and rmnJ(CH)(n=1, 2, 3, 4) were predicted well using the larger 6-31+G(d,p) and 6-311++G(d,p) basis sets and at the B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p), B3LYP/6-31+G(2d,2p) levels of theory. The computed atomic charges [Mülliken; Natural Bond Orbital Analysis (NBO); Merz-Kollman (MK); CHELP and CHELPG] for the B3LYP/6-311++G(d,p) geometry optimized structures of 1-17 were used to explore correlations with the experimental proton and carbon chemical shifts.     

Role of singlet diradicals in reactions of 2-carbenabicyclo[3.2.1]octa-3,6-diene

The generation of 2-carbenabicyclo[3.2.1]octa-3,6-diene (1) results in the formation of C(8)H(8) hydrocarbons endo-6-ethynylbicyclo[3.1.0]hex-2-ene (4), semibullvalene (5), and 5-ethynyl-1,3-cyclohexadiene (6), and C(8)H(10) hydrocarbons bicyclo[3.2.1]octa-2,6-diene (7), tricyclo[3.2.1.0(4,6)]oct-2-ene (8), and tetracyclo[3.3.0.0(2,8)0(4,6)]octane (9). Focus is placed on three mechanistic pathways for the formation of the C(8)H(10) hydrocarbon fraction: (a) abstraction of hydrogen by triplet carbene 1T to produce an equilibrating set of monoradicals, (b) interconversion of triplet carbene 1T into tricyclic triplet diradical 19T and tetracyclic triplet diradical 20T, and (c) interconversion of singlet 1S with analogous singlet diradical 19S and 20S. Ab initio calculations at the (U)B3LYP/6-311+G(3df,2p)//(U)B3LYP/6-31G(d,p) and broken spin symmetry UBS B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d,p) levels rule out choices (a) and (b) and are consistent with the singlet diradical process.     

Substituent effects on the acidity of weak acids. 2. Calculated gas-phase acidities of substituted benzoic acids

To investigate the origin of substituent effects on the acidity of benzoic acids, the structures of a series of substituted benzoic acids and benzoates have been calculated at the B3LYP/6-311+G* and MP2/6-311+G* theoretical levels. The vibrational frequencies were calculated using B3LYP/6-311+G* and allowed corrections for the change in zero-point energies on ionization, and the change in energy on going from 0 K (corresponding to the calculations) to 298 K. A more satisfactory agreement with the experimental values was obtained by energy calculations at the MP2/ 6-311++G* level using the above structures. The resulting Delta H(acid) values agree very well with the experimental gas-phase acidities. The energies of compounds with pi-electron-accepting or -releasing substituents, rotated to give the transition state geometries, provided rotational barriers that could be compared with those found for the corresponding substituted benzenes. Isodesmic reactions allowed the separate examination of the substituent effects on the energies of the acids and on the anions. Electron-withdrawing groups stabilize the benzoate anions more than they destabilize the benzoic acids. Electron-donating groups stabilize the acids and destabilize the anions by approximately equal amounts. The gas-phase acidities of meta- and para-substituted benzoic acids are linearly related. This is also found for the acidities of substituted phenylacetic acids and benzoic acids. Since direct pi-electron interactions are not possible with the phenylacetic acids, this indicates that the acidities are mainly controlled by a field effect interaction between the charge distribution in the substituted benzene ring and the negative charge of the carboxylate group. The Hammett sigma(M) and sigma(P) values are also linearly related for many small substituents from NO(2) through the halogens and to OH and NH(2). Most of the other substituents fall on a line with a different slope     

丁烯和丁烷自由基阳离子的分子结构和超精细结构的 理论研究

用密度函数理论B3LYP方法和6-31G(d,p),6-311G(d,p)及6-311+G(d,p)基组，分别对1-C4H^+~8,2-C4H^+~8和C4H^+~10进行了构型优化和频率分析计算，预言1-C4H^+~8具有非平面构型，与以往报道的从头算和密度函数理论计算结果不同。在各自由基阳离子的B3LYP构型上，进行了B3LYP、MP2及MRSDCI方法的超精细偶合常数计算，得到了比以往更好的结果，特别是MP2/B3LYP计算值是至今与实验值符合得最好的理论计算结果。     

Remarks on GIAO-DFT predictions of 13C chemical shifts

Predicting (13)C chemical shifts by GIAO-DFT calculations appears to be more accurate than frequently expected provided that: (a) the comparison between experimental and theoretical data is performed using the linear regression method, (b) a sufficiently high level of theory [e.g. B3LYP/6-311 + + G(2d,p)//B3LYP/6-311 + + G(2d,p) or PBE1PBE/6-311 + G(2df,p)//B3LYP/6-311 + + G(2d,p)] is used, (c) the experimental data originate from the measurements performed in one solvent whose influence is taken into account at the molecular geometry optimization step and, first of all, during the shielding calculation, (d) the experimental data are free of heavy atom effects or such effects are appropriately treated in calculations, and finally (e) the conformational compositions of the investigated objects are known.     

Comprehensive density functional theory study on serine and related ions in gas phase: conformations, gas phase basicities, and acidities

Density functional theory (DFT) calculations have been performed to investigate the gas-phase conformations of serine and its three related ions (serineH(+), serine(-), and serine(2-)). The full ensemble of possible conformations, 324 conformations for serine, 108 for serineH(+), 162 for serine(-) and 54 for serine(2-), were first surveyed at B3LYP/6-31G level, and then the obtained unique conformations were further refined at B3LYP/6-311+G level. From full optimizations, 74 unique conformations for seine, 14 for serineH(+), 11 for serine(-), and 4 for serine(2-) were located, and their relative energies were also determined at B3LYP/6-311+G level. Atoms in molecules (AIM) analysis was carried out to establish rigorous definition of hydrogen bonds. Six types of intramolecular H-bonds in conformers of serine, six types in serineH(+), three types in serine(-), and two types in serine(2-) were identified within the framework of AIM theory and their relative strengths were determined based on topological properties at bond critical points (BCPs) of H-bonds. The intramolecular H-bonds were demonstrated to play an important role in deciding the relative stability of conformations of amino acids and the related ions. The enthalpies and Gibbs free energies of protonation and deprotonation reactions of serine and its related ions were calculated at B3LYP/6-311+G//B3LYP/6-31G, and B3LYP/6-311+G//B3LYP/6-311+G level. The calculated results are both in excellent agreement with the experimental data. We demonstrate in this study that B3LYP is an efficient and accurate method to predict the thermochemical and structural parameters of amino acids and the related ions.     

Partially bridge-fluorinated dimethyl bicyclo[1.1.1]pentane-1,3-dicarboxylates: preparation and NMR spectra

Direct fluorination of dimethyl bicyclo[1.1.1]pentane-1,3-dicarboxylate, obtained from [1.1.1]propellane prepared by an improved synthetic procedure, furnished esters of 14 of the 15 possible bridge-fluorinated bicyclo[1.1.1]pentane-1,3-dicarboxylic acids, isolated by preparative GC. Calculated geometries reflect the substitution pattern in a regular fashion compatible with Bent's rules. Considerable additional strain is introduced into the bicyclo[1.1.1]pentane cage by polyfluorination; it is calculated to be as high as 33-35 kcal/mol for hexasubstitution. Three arrangements of the fluorine substituents are especially strain-rich: geminal, proximate, and W-related. The (1)H, (13)C, and (19)F NMR spectra exhibit a striking variety of chemical shifts and long-range coupling constants. These are in good agreement with results calculated with neglect of the bridgehead substituents for all of the chemical shifts by the GIAO-RHF/6-31G//RHF/6-31G and GIAO-RHF/6-31G//MP2/6-31G methods and for many of the coupling constants by the EOM-CCSD/6-311G//MP2/6-311G method. The proximate (4)J(FF) constants are particularly large (50-100 Hz) and show an inverse linear dependence on the calculated F-F distance in the range 2.43-2.58 A.     

7-Ethyl-2,3,5,6,8-pentahydroxy-1,4-naphthoquinone (echinochrome A): a DFT study of the antioxidant mechanism 2.* The structure of monosodium salts of echinochrome A and their reactions with the hydroperoxyl radical

The relative gas-phase acidities of all OH groups of 7-ethyl-2,3,5,6,8-pentahydroxy-1,4-naphthoquinone (echinochrome A, 1) were evaluated by the B3LYP/6-311G(d) and B3LYP/6-311G(d,p) methods. Calculations predict that gB-OH groups at the C(2) and C(6) atoms are the most acidic in molecule 1and their acidity is higher than that of o-nitrophenol. Conformational analysis of undissociated monosodium salts of 1and their radicals was performed. It was shown that gas-phase quenching reactions of the hydroperoxyl radical by mono-sodium salts of 1are exothermic.     

Structural elucidation of nitro-substituted five-membered aromatic heterocycles utilizing GIAO DFT calculations

The GIAO (Gauge Including Atomic Orbitals) DFT (Density Functional Theory) method is applied at the B3LYP/6-31+G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311++G(d,p)//B3LYP/6-31+G(d), B3LYP/6-311+G (2d,p)//B3LYP/6-31+G(d) and B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) levels of theory for the calculation of proton and carbon chemicals shifts and coupling constants for 25 nitro-substituted five-membered heterocycles. Difference (1D NOE) spectra in combination with long-range gHMBC experiments were used as tools for the structural elucidation of nitro-substituted five-membered heterocycles. The assigned NMR data (chemical shifts and coupling constants) for all compounds were found to be in good agreement with theoretical calculations using the GIAO DFT method. The magnitudes of one-bond (1JCH) and long-range (nJCH, n>1) coupling constants were utilized for unambiguous differentiation between regioisomers of nitro-substituted five-membered heterocycles.     

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。     

DFT法研究3-羟基丙烯醛的双键旋转异构反应机理

利用密度泛函理论(DFT)分别在B3LYP/6-31G**和B3LYP/6-311＋＋G**的计算水平上优化了基态3-羟基丙烯醛分子在双键旋转异构反应过程中的平衡态以及过渡态的几何构型，分析了反应过程中键参数的变化，计算了该反应的内禀反应坐标(IRC)，发现在重排反应途径上存在一个四元环骨架的中间体.通过振动分析对平衡态和过渡态进行了确认，并得到了零点能.计算结果表明，基态3-羟基丙烯醛分子的双键旋转异构反应经过两步完成，第一步反应位垒稍高，第二步反应位垒较低，存在着发生重排反应的可能性.