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.     

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.     

Theoretical study of the conformational energy hypersurface of cyclotrisarcosyl

The multidimensional Conformational Potential Energy Hypersurface (PEHS) of cyclotrisarcosyl was comprehensively investigated at the DFT (B3LYP/6-31G(d), B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p)), levels of theory. The equilibrium structures, their relative stability, and the Transition State (TS) structures involved in the conformational interconversion pathways were analyzed. Aug-cc-pVTZ//B3LYP/6-311++G(d,p) and MP2/6-31G(d)//B3LYP/6-311++G(d,p) single point calculations predict a symmetric cis-cis-cis crown conformation as the energetically preferred form for this compound, which is in agreement with the experimental data. The conformational interconversion between the global minimum and the twist form requires 20.88 kcal mol-1 at the MP2/6-31G(d)//B3LYP/6-311++G(d,p) level of theory. Our results allow us to form a concise idea about the internal intricacies of the PEHSs of this cyclic tripeptide, describing the conformations as well as the conformational interconversion processes in this hypersurface. In addition, a comparative analysis between the conformational behaviors of cyclotrisarcosyl with that previously reported for cyclotriglycine was carried out     

Hydride affinity scale of various substituted arylcarbeniums in acetonitrile

Combined with the integral equation formalism polarized continuum model (IEFPCM), the hydride affinities of 96 various acylcarbenium ions in the gas phase and CH(3)CN were estimated by using the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-311++G(2df,2p)//B3LYP/6-31+G(d), and BLYP/6-311++G(2df,2p)//B3LYP/6-31+G(d) methods for the first time. The results show that the combination of the BLYP/6-311++G(2df,2p)//B3LYP/6-31+G(d) method and IEFPCM could successfully predict the hydride affinities of arylcarbeniums in MeCN with a precision of about 3 kcal/mol. On the basis of the calculated results from the BLYP method, it can be found that the hydride affinity scale of the 96 arylcarbeniums in MeCN ranges from -130.76 kcal/mol for NO(2)-PhCH(+)-CN to -63.02 kcal/mol for p-(Me)(2)N-PhCH(+)-N(Me)(2), suggesting most of the arylcarbeniums are good hydride acceptors. Examination of the effect of the number of phenyl rings attached to the carbeniums on the hydride affinities shows that the increase of the hydride affinities takes place linearly with increasing number of benzene rings in the arylcarbeniums. Analyzing the effect of the substituents on the hydride affinities of arylcarbeniums indicates that electron-donating groups decrease the hydride affinities and electron-withdrawing groups show the opposite effect. The hydride affinities of arylcarbeniums are linearly dependent on the sum of the Hammett substituent parameters σ(p)(+). Inspection of the correlation of the solution-phase hydride affinities with gas-phase hydride affinities and aqueous-phase pK(R)(+) values reveals a remarkably good correspondence of ΔG(H(-)A)(R(+)) with both the gas-phase relative hydride affinities only if the α substituents X have no large electron-donating or -withdrawing properties and the pK(R)(+) values even though the media are dramatically different. The solution-phase hydride affinities also have a linear relationship with the electrophilicity parameter E, and this dependence can certainly serve as one of the most effective ways to estimate the new E values from ΔG(H(-)A)(R(+)) or vice versa. Combining the hydride affinities and the reduction potentials of the arylcarbeniums, we obtained the bond homolytic dissociation Gibbs free energy changes of the C-H bonds in the corresponding hydride adducts in acetonitrile, ΔG(HD)(RH), and found that the effects of the substituent on ΔG(HD)(RH) are very small. Simple thermodynamic analytic platforms for the three C-H cleavage modes were constructed. It is evident that the present work would be helpful in understanding the nature of the stabilities of the carbeniums and mechanisms of the hydride transfers between carbeniums and other hydride donors.     

On the flexibility of beta-peptides

The full conformational space was explored for an achiral and two chiral beta-peptide models: namely For-beta-Ala-NH2, For-beta-Abu-NH2, and For-beta-Aib-NH2. Stability and conformational properties of all three model systems were computed at different levels of theory: RHF/3-21G, B3LYP/6-311++G(d,p)//RHF/3-21G, B3LYP/6-311++G(d,p), MP2//B3LYP/6-311++G(d,p), CCSD//B3LYP/6-311++G(d,p), and CCSD(T)//B3LYP/6-311++G(d,p). In addition, ab initio E = E(phi, micro, psi) potential energy hypersurfaces of all three models were determined, and their topologies were analyzed to determine the inherent flexibility properties of these beta-peptide models. Fewer points were found and assigned than expected on the basis of Multidimensional Conformational Analysis (MDCA). Furthermore, it has been demonstrated, that the four-dimensional surface, E = E(phi, mu, psi), can be reduced into a three-dimensional one: E = E[phi, f(phi), psi]. This reduction of dimensionality of freedom of motion suggests that beta-peptides are less flexible than one would have thought. This agrees with experimental data published on the conformational properties of peptides composed of beta-amino acid residues.     

Theoretical investigation on the GaCl3-catalyzed ring-closing metathesis reaction of N-2,3-butadienyl-2-propynyl-1-amine: three-membered ring versus four-membered ring mechanism

The gallium chloride (GaCl(3))-catalyzed ring-closing metathesis reaction mechanism of N-2,3-butadienyl-2-propynyl-1-amine has been studied at the Becke three-parameter hybrid functional combined with Lee-Yang-Parr correlation functional (B3LYP)/6-31G(d), B3LYP/6-31+G(d,p), B3LYP/6-311++G(d,p)//B3LYP/ 6-31G(d) and the second-order M?ller-Plesset perturbation (MP2)/6-311++G(d,p)//B3LYP/6-31+G(d,p) levels. It was found that the final metathesis product can be yielded via a three-membered or four-membered ring mechanism. The three-membered ring pathway is favorable due to its low energy barrier at the rate determining step. The whole reaction is stepwise and strongly exothermic.     

Theoretical studies on dynamics and thermochemistry of the reactions CF(3)CHCl(2)+Cl-->CF(3)CCl(2)+HCl and CF(3)CHFCl+Cl-->CF(3)CFCl+HCl

A dual-level direct dynamics study has been carried out for the two hydrogen abstraction reactions CF(3)CHCl(2)+Cl and CF(3)CHFCl+Cl. The geometries and frequencies of the stationary points are optimized at the BHLYP/6-311G(d,p), B3LYP/6-311G(d,p), and MP2/6-31G(d) levels, respectively, with single-point calculations for energy at the BHLYP/6-311++G(3df,2p), G3(MP2), and QCISD(T)/6-311G(d,p) levels. The enthalpies of formation for the species CF(3)CHCl(2), CF(3)CHFCl, CF(3)CCl(2), and CF(3)CFCl are evaluated at higher levels. With the information of the potential energy surface at BHLYP/6-311++G(3df,2p)//6-311G(d,p) level, we employ canonical variational transition-state theory with small-curvature tunneling correction to calculate the rate constants. The agreement between theoretical and experimental rate constants is good in the measured temperature range 276-382 K. The effect of fluorine substitution on reactivity of the C-H bond is discussed.     

The nature and role of 8-deltacyclyl and 7-isodeltacyclyl cations in solvolytic reactions of parent brosylates

Solvolysis of exo-8-deltacyclyl brosylate proceeds directly through a C(2) delocalized cation to exo-8-deltacyclyl acetate. The solvolysis of the endo epimer presents a more complex picture, reacting via a classical deltacyclyl cation, the nonclassical C(2) delocalized cation, and the isodeltacyclyl cation. The solvolysis of exo-7-isodeltacyclyl brosylate generates the 7-isodeltacyclyl ion and subsequently the C(2) delocalized deltacyclyl cation forming 8-deltacyclyl acetate and exo-7-isodeltacyclyl acetate. The cationic intermediates in these three related reaction manifolds are characterized using density functional methods at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) and BPW91/6-311+G(3df, 2p)//BPW91/6-31G(d) levels.     

DFT study on mechanism of the classical Biginelli reaction

The condensation of benzaldehyde, urea, and ethyl acetoacetate according to the procedure described by Biginelli was investigated at the B3LYP/6-31G（d）, B3LYP/6-31 ＋G（d,p）, and B3LYP/6-311＋G（3df,2p）//B3LYP/6-31＋G（d,p） levels to explore the reaction mechanism. According to the mechanism proposed by Kappe, structures of five intermediates were optimized and four transition states were found. The calculation results proved that the mechanism proposed by Kappe is right.     

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.     

Theoretical and experimental study of the absolute configuration of helical structure of (2R,3S)-Rubiginone A2 analog

A novel analogue of (2R,3S)-Rubiginone A₂ was synthesized as a chiral helical model compound via an eight-step procedure (2.7% overall yield). Quantum methods, such as density functional theory (DFT) at different basis sets of 6-311+(d), 6-311++G(2d,p), were used to compute its optical rotation and electronic circular dichroism at the B3LYP/6-311++G(2d,p) level in the gas phase and in solution using PCM model, respectively. UV corrections were performed in electronic circular dichroism (ECD) simulations to match the experimental ECD well. The suitable computational methods, e.g., B3LYP/6-311++G(2d,p)//B3LYP/6-311++G(2d,p) in the gas phase using zero-point energy in Boltzmann statistics, were found and suggested for optical rotation and circular dichroism computations that can be used for absolute configuration determination of chiral helical compounds.     

Neutral homoaromaticity in some heterocyclic systems

[reaction: see text] Neutral homoaromaticity has been evaluated in heterocyclic systems related to the bicyclo[3.2.1]octane skeleton with replacement of CH(2) at C-2 in bicyclo[3.2.1]octa-3,6-diene with X = BH, AlH, Be, Mg, O, S, PH, NH (12); replacement of CH at C-3 in bicyclo[3.2.1]octa-3,6-dien-2-yl anion with PH, S, NH, O (13); and replacement at C-2 and C-3 with N and O (14). Stabilization energies (SE) are evaluated using density functional theory and homodesmotic equations at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d) level for series 12-14. Stabilization energies are compared with diamagnetic susceptibility exaltations, Lambda, CSGT-B3LYP/6-31G(d)//B3LYP/6-31G(d), and nucleus-independent chemical shifts (NICS), GIAO-B3LYP/6-311+G(2d,p)//B3LYP/6-31G(d). Analysis of frontier orbitals and geometries, B3LYP/6-31G(d)//B3LYP/6-31G(d), and proton affinities of 2-azabicyclo[3.2.1]octa-3,6-diene, pyrrole, and related model systems, B3LYP/6-311+G(2d,2p)//B3LYP/6-31G(d), provide complementary evidence supporting the division of the substrates evaluated into antihomoaromatic (12, X = BH, AlH, and Be), nonhomoaromatic (12, X = O, S, NH, PH), and homoaromatic (13, X = S, PH, NH, O and 14 X = ON), with 12 (X = Mg) appearing as transitional between anti- and nonhomoaromatic.     

Kinetics of the multichannel reaction of methanethiyl radical (CH3S*) with 3O2

The CH3S* + O2 reaction system is considered an important process in atmospheric chemistry and in combustion as a pathway for the exothermic conversion of methane-thiyl radical, CH3S*. Several density functional and ab initio computational methods are used in this study to determine thermochemical parameters, reaction paths, and kinetic barriers in the CH3S* + O2 reaction system. The data are also used to evaluate feasibility of the DFT methods for higher molecular weight oxy-sulfur hydrocarbons, where sulfur presents added complexity from its many valence states. The methods include: B3LYP/6-311++G(d,p), B3LYP/6-311++G(3df,2p), CCSD(T)/6-311G(d,p)//MP2/6-31G(d,p), B3P86/6-311G(2d,2p)//B3P86/6-31G(d), B3PW91/6-311++G(3df,2p), G3MP2, and CBS-QB3. The well depth for the CH3S* + 3O2 reaction to the syn-CH3SOO* adduct is found to be 9.7 kcal/mol. Low barrier exit channels from the syn-CH3SOO* adduct include: CH2S + HO2, (TS6, E(a) is 12.5 kcal/mol), CH3 + SO2 via CH3SO2 (TS2', E(a) is 17.8) and CH3SO + O (TS17, E(a) is 24.7) where the activation energy is relative to the syn-CH3SOO* stabilized adduct. The transition state (TS5) for formation of the CH3SOO adduct from CH3S* + O2 and the reverse dissociation of CH3SOO to CH3S* + O2 is relatively tight compared to typical association and simple bond dissociation reactions; this is a result of the very weak interaction. Reverse reaction is the dominant dissociation path due to enthalpy and entropy considerations. The rate constants from the chemical activation reaction and from the stabilized adduct to these products are estimated as functions of temperature and pressure. Our forward rate constant and CH3S loss profile are in agreement with the experiments under similar conditions. Of the methods above, the G3MP2 and CBS-QB3 composite methods are recommended for thermochemical determinations on these carbon-sulfur-oxygen systems, when they are feasible.     

A new scheme for determining the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of glycine and alanine peptides

In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.     

类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应

采用DFT B3LYP和QCISD方法研究了类硅烯H2C＝SiLiBr与RH (R＝F, OH, NH2)的插入反应. 在B3LYP/6- 311＋G(d,p)水平上优化了反应势能面上的驻点构型. 结果表明, H2C＝SiLiBr与HF, H2O或NH3发生插入反应的机理相同. QCISD/6-311＋＋G(d,p)//B3LYP/6-311＋G(d,p)计算的三个反应的势垒分别为148.62, 164.42和165.07 kJ•mol－1, 反应热分别为－69.63, －43.02和－28.27 kJ•mol－1. 相同条件下发生插入反应时, 反应活性都是H—F＞H—OH＞H—NH2.     

第一性原理方法预测水相核酸碱基及其代谢物的氧化还原电动势

氧化还原电动势是了解核酸中电荷/电子转移过程以及设计具有新型氧化还原活性的碱基类化合物的重要参数. 本文对82个芳香化合物的氧化还原电动势进行理论预测, 通过计算值和实验值的比较发现: 气相采用B3LYP/6-311++G(2df,2p)//B3LYP/6-31+G(d)方法, 液相采用HF-COSMORS/UAHF方法, 对运用HF- CPCM/UAHF方法在水相重新优化的构型计算溶剂化能, 能有效预测芳香化合物水相氧化还原电动势, 该理论方法计算的绝对均方根误差(RMSD)为0.124 V. 运用该理论方法成功预测了属于芳香化合物的核酸碱基及其代谢物的水相氧化还原电动势. 根据预测结果, 讨论了核酸中电荷/电子转移过程以及结构改变对设计具有新型氧化还原活性的核酸碱基类化合物的影响. 本文为设计具有氧化还原活性的新型核酸碱基类化合物提供了一种理论方法.     

Further evidence for the inseparability of the theoretical enthalpic terminal and penultimate unit effects in the radical copolymerization of styrene with acrylonitrile

The theoretical enthalpies of propagation reactions at 0 K without zero‐point vibrational energy corrections according to terminal and penultimate models of the radical copolymerization of styrene with acrylonitrile are reported from molecular orbital calculations at the following levels of theory and basis sets: HF/6‐31G(d); B3‐LYP/6‐31G(d); B3‐LYP/6‐311G(d,p) and B3‐LYP/6‐311+G(3df)//6‐311G(d,p). Both the enthalpic terminal and penultimate unit effects, determined according to the theoretical thermochemistry, depend on the level of theory and basis set used for the molecular orbital calculations. The best performing B3LYP/6‐311+G(3df)//B3LYP/6‐311G(d,p) procedure gives theoretical enthalpies for the addition of styrene and acrylonitrile to CH that differ from experimental values by 0.6 and 1.6 kcal mol^?1, respectively. An analysis of the results obtained here leads to the conclusion that at least for the styrene–acrylonitrile monomer system, that is, a monomer system known as one of the few systems that do not conform to terminal model composition and microstructure equations, the enthalpic terminal unit effects seem to depend on the penultimate units of the growing radical. This finding, together with the outcome from our previous work on the dependence of the penultimate effects on the terminal units in a growing macroradical, indicates the inseparability of the enthalpic terminal (implicit) and explicit penultimate unit effects on the radical copolymerization. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 1778–1787, 2003     

The Dowd-Beckwith ring expansion: a theoretical study

UB3LYP/6-311++G(d,p) and ROMP2/6-311++G(d,p)//UB3LYP/6-311++G(d,p) calculations including the effect of benzene solvent through the PCM-UAHF method render a concerted mechanism without fragmentation as the most favourable one for the Dowd-Beckwith radical ring expansion of the bromomethyl adduct of methyl cyclopentanone-2-carboxylate to yield methyl cyclohexanone-3-carboxylate. The corresponding concerted TS is a bicyclic alcoxy radical.     

Density functional study of the conformations and intramolecular proton transfer in thiohydroxamic acids

The conformational preferences of thiohydroxamic acids (N-hydroxythioamides) are investigated by the density functional B3LYP/6-311++G(3df,3pd)//B3LYP/6-31G(d) method in this work. Unlike hydroxamic acids, the thione and thiol forms are found to be equally stable in the gas phase, and the reaction pathways for the interconversion between the thione and thiol forms have been deduced to involve rotation about the C[double bond, length as m-dash]N bond of the thiol tautomer in the rate-determining step. The effect of aqueous solvation on the reactions has also been investigated. It is found that inclusion of a few explicit water molecules in an implicit solvent calculation is necessary in order to accurately account for hydrogen bonding effects. Thiohydroxamic acids, like their hydroxamic acid analogues, are found to be N-acids, both in the gas phase and in aqueous solution.     

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.