Ab initio calculations on 1,2-hydrogen shifts in the benzene radical cation and on carbon scrambling via an isomerization to the fulvene structure

Multireference configuration interaction (MRCI//6-31G**) ab initio calculations show that the barrier for hydrogen scrambling in the benzene radical cation is about 50 kcal mol^?1. Once the internal energy is sufficient for a 1,2-hydrogen shift, the moving hydrogen can go to any position in the ring. The barrier for carbon scrambling via an isomerization to the fulvene structure is about 17 kcal mol^?1 higher than that for hydrogen scrambling. Both of these values are far below the dissociation limit.     

Structural aspects of phencyclidines: crystal structure and quantum mechanical calculations for 1-[1-(2-thienyl)cyclohexyl] piperidine and its hydrochloride

Crystal structure determinations for neutral and protonated phencyclidine, 1-[1-(2-thienyl)cyclohexyl] piperidine, show that the piperidine-axial conformer on the cyclohexane ring is present in the neutral compound, and that the piperidine-equatorial conformer in the protonated species. Quantum mechanical calculations in vacuo using ab initio techniques also arrive at the same conclusion. A search of the crystallographic literature via the Cambridge structural database reveals that all protonated phencyclidines assume the piperidine-equatorial conformation, and most neutral phencyclidines assume the piperidine-axial conformation.     

The nature of halogen...halogen synthons: crystallographic and theoretical studies

A study of the halogen...halogen contacts in organic compounds using ab initio calculations and the results of previously reported crystallographic studies show that these interactions are controlled by electrostatics. These contacts can be represented by the geometric parameters of the C--X1...X2--C moieties (where theta1=C--X1...X2 and theta2=X1...X2--C; ri=X1...X2 distance). The distributions of the contacts within the sum of van der Waals radii (rvdW) versus thetai (theta1=theta2) show a maximum at theta approximately 150 degrees for X=Cl, Br, and I. This maximum is not seen in the distribution of F...F contacts. These results are in good agreement with our ab initio calculations. The theoretical results show that the position of the maximum depends on three factors: 1) The type of halogen atom, 2) the hybridization of the ipso carbon atom, and 3) the nature of the other atoms that are bonded to the ipso carbon atom apart from the halogen atom. Calculations show that the strength of these contacts decreases in the following order: I...I>Br...Br>Cl...Cl. Their relative strengths decrease as a function of the hybridization of the ipso carbon atom in the following order: sp2>sp>sp3. Attaching an electronegative atom to the carbon atom strengthens the halogen...halogen contacts. An electrostatic model is proposed based on two assumptions: 1) The presence of a positive electrostatic end cap on the halogen atom (except for fluorine) and 2) the electronic charge is anisotropically distributed around the halogen atom.     

二氮双环阳离子游离基中N,N'-三电子键

用从头算HF/3-21+G^*优化了二氮双环[m,n,l]游离基阳离子(m,n,l≥2～5)。分子[4,4,4]和[2,2,2]^+.,[3,3,3]^+.,[4,4,4]^+.游离基阳离子的优势构型有D3对称性,而其它游离基阳离子的优势构型为非对称性。通过比较这些阳离子几何构型,HOMO和NHOMO(即NextHOMO和HOMO-1),和由MNDO计算确定的原子对作用能,表明当二氮双环游离基阳离子的桥链(CH2)n的n≥3时,桥头氮原子通过空间相互用用形成了一个弱的N,N'-三电子σ键。形成的三电子键强度不随环的扩大而增强。而三电子键强度被两个因素影响：一个是桥头氮原子间的p轨道重叠的取向;另一个是它们相应p轨道成分。     

Ab initio evidence for the stepwise mechanism of the McLafferty rearrangement of the butanal radical cation

The mechanism of the McLafferty rearrangement of the butanal radical cation to ethylene and vinyl alcohol cation is found, by ab initio calculations, to be stepwise. The results of a previous ab initio study are inconclusive because of symmetry restriction in their geometry optimization.     

Electronic structure and conformational properties of the amide linkage Part 5. Internal rotation and inversion in 1-formylaziridine

Internal rotation and nitrogen inversion in 1-formylaziridine (1) have been investigated by quantum mechanical (ab initio and MNDO) calculations, especially with respect to the variation of the geometry of the aziridine ring. While conformational stability is mainly determined by the n(N)/π(CO) interaction, the bond lengths within the ring are affected by the amount of interaction between the π(CO) orbital and the Walsh orbital ω_A. To separate the two types of interaction, calculations were also performed on formylcyclopropane (9). The torsional potential of 1 has a minimum close to the perpendicular conformation 1b. The two bisected conformations, 1a and 1c, are transition states for internal rotation. For nitrogen inversion, a barrier of 1.44 kcal mol⁻¹ (ab initio) was calculated. Calculations on 1-cyanoaziridine (7) gave inversion barriers of 5.81 (ab initio) and 12.31 kcal mol⁻¹ (MNDO). Probably due to methodical reasons the ab initio values seem to be too low, as calculations with different basis sets for aziridine indicate.     

Structure and conformation of cyclobutylsilane: an electron diffraction and ab initio study

A gas electron diffraction study of cyclobutylsilane results in a mixture of equatorial and axial conformers, with the equatorial confomer slightly more stable (Δ G = 0.8 ± 0.4 kJ mol⁻¹). The cyclobutyl ring is distorted with the adjacent bonds longer (C₁---C₂ = 1.573 (4) Å) than the opposite bonds (C₂---C₃ = 1.557 (4) Å). The experimental values for the energy difference between the two conformers and for the geometric parameters are reproduced very well by ab initio calculations. The importance of silicon 3d orbitals in the interpretation of ring distortion is ambiguous, but on the basis of the ab initio calculations the participation of silicon 3d functions is negligible.     

Solution and biologically relevant conformations of enantiomeric 11-cis-locked cyclopropyl retinals

To gain information on the conformation of the 11-cis-retinylidene chromophore bound to bovine opsin, the enantiomeric pair (2a and 2b) of 11-cis-locked bicyclo[5.1.0]octyl retinal (retCPr) 2 was prepared and its conformation was investigated by NMR, geometry optimization, and CD calculations. This compound is also of interest since it contains a unique moiety in which a chiral cyclopropyl group is flanked by triene and enal chromophores, and hence would clarify the little-known chiroptical contribution of a cyclopropyl ring linked to polyene systems. NMR revealed that the seven-membered ring of retCPr adopts a twist chair conformation. The NMR-derived structure constraints were then used for optimizing the geometry of 2 with molecular mechanics and ab initio methods. This revealed that enantiomer 2a with a 11 beta,12 beta-cyclopropyl group exists as two populations of diastereomers depending on the twist around the 6-s bond; however, the sense of twist around the 12-s is positive in both rotamers. The theoretical Boltzmann-weighted CD obtained with the pi-SCF-CI-DV MO method and experimental spectra were consistent, thus suggesting that the conjugative effect of the cyclopropyl moiety is minimal. It was found that only the beta-cyclopropyl enantiomer 2a, but not the alpha-enantiomer 2b, binds to opsin. This observation, together with earlier retinal analogues incorporation results, led to the conclusion that the chromophore sinks into the N-terminal of the opsin receptor from the side of the 4-methylene and 15-aldehyde, and that the binding cleft accommodates 11-cis-retinal with a slightly positive twist around C12/C13. A reinterpretation of the previously published negative CD couplet of 11,12-dihydrorhodopsin also leads to a chromophoric C12/C13 twist conformation with the 13-Me in front as in 1b. Such a conformation for the chromophore accounts for both the observed biostereoselectivity of retCPr 2a and the observed negative couplet of 11,12-dihydro-Rh7.     

12‐ to 22‐Membered Bridged β‐Lactams as Potential Penicillin‐Binding Protein Inhibitors

As potential inhibitors of penicillin‐binding proteins (PBPs), we focused our research on the synthesis of non‐traditional 1,3‐bridged β‐lactams embedded into macrocycles. We synthesized 12‐ to 22‐membered bicyclic β‐lactams by the ring‐closing metathesis (RCM) of bis‐ω‐alkenyl‐3(S)‐aminoazetidinone precursors. The reactivity of 1,3‐bridged β‐lactams was estimated by the determination of the energy barrier of a concerted nucleophilic attack and lactam ring‐opening process by using ab initio calculations. The results predicted that 16‐membered cycles should be more reactive. Biochemical evaluations against R39 DD‐peptidase and two resistant PBPs, namely, PBP2a and PBP5, revealed the inhibition effect of compound 4d , which featured a 16‐membered bridge and the N‐tert‐butyloxycarbonyl chain at the C3 position of the β‐lactam ring. Surprisingly, the corresponding bicycle, 12d , with the PhOCH₂CO side chain at C3 was inactive. Reaction models of the R39 active site gave a new insight into the geometric requirements of the conformation of potential ligands and their steric hindrance; this could help in the design of new compounds.     

Structure of the HOOO radical in liquid water: a theoretical study.

The HOOO radical is supposed to play a role in ozone chemistry, both in the gas phase and aqueous media. We discuss the influence of the solvent on the electronic and geometrical structure of this radical using density functional and high-level ab initio calculations together with continuum, discrete, and discrete-continuum solvent models. Solute-solvent electrostatic interactions are shown to be fundamental, and lead to a noticeable stabilization of the radical, which should adopt a trans conformation in aqueous media. In fact, no energy minimum for the cis conformation is predicted in these conditions.     

烯烃分子在氢终止Si(100)-2×1表面的自由基链反应

应用密度泛函理论(DFT)和从头计算分子动力学方法(ab initio MD)研究了不饱和烯烃在氢终止的Si(100)-2×1表面的自由基链反应. 计算表明, 自由基链反应中重要的一步是烷烃链自由基的氢抽提过程, 硅表面上邻近位置(the nearest neighbor, NN)的氢抽提比次邻近位置(the next-nearest neighbor, NNN)的氢抽提有一稍低的能垒. 从头算分子动力学显示, 过渡态的烷烃自由基与氢终止Si(100)-2×1表面上的氢原子能够很容易形成C—H键, 完成一个氢抽提过程, 同时在硅表面产生下一个孤电子, 继续引发链反应.     

LaC4团簇的理论研究

应用量子化学从头算方法研究了LaC4团簇，结果表明，在所提出的构型中，稀土位于碳环上最稳定，计算得到该团簇的绝热电子亲和势为81．05kJ/mol，离化能为628．88kJ/mol。该结果解决了实验中无法测定的问题，同时为合成实验提供了一定的理论指导。     

An ab initio and density functional theory study of radical-clock reactions

Density functional theory (DFT) and ab initio (CBS-RAD) calculations have been used to investigate a series of "radical clock" reactions. The calculated activation energies suggest that the barriers for these radical rearrangements are determined almost exclusively by the enthalpy effect with no evidence of significant polar effects. The ring-closure reactions to cyclopentylmethyl radical derivatives and the ring opening of cyclopropylmethyl radicals give different correlations between the calculated heat of reaction and barrier, but the two types of reaction are internally consistent.     

Vibrational assignment of the normal modes of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one via FTIR and Raman spectra, and ab inito calculations

Raman and FTIR spectra of 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one were recorded in the regions, 100-3300 and 400-4000 cm(-1), respectively. Vibrational frequencies and intensities of the fundamental modes of this hetrocyclic organic molecule were computed using ab initio as well as AM1 semiempirical molecular orbital methods. Ab initio calculations were carried out with basis set up to RHF/6-311G. Conformational studies regarding the effect of moving the methoxy group in the 2-phenyl-4-(4-methoxy benzylidene)-2-oxazolin-5-one molecule to a different position on the ring was also carried out. Observed vibrational wavenumbers were found to be mostly consistent with ab initio values. The most intense mode of vibration observed at 1250 cm(-1) in Raman spectra, also observed as a strong band in FTIR, was assigned as C-O stretching vibration in the methoxy group. Asymmetric stretching vibrations between CC and CN bonds was predicted as most intense mode by our ab initio calculation.     

The 3-Thioxo-1,2-Dithiol-4-yl Group: A Versatile One Endowed Also With a –R Electronic Effect

The pK_a values in an aqueous solution of some 4-aminodithiolethiones, 4-aminodithiolones, 5-phenyl-4-hydroxydithiolethione, and 5-phenyl-4-hydroxydithiolone were determined by UV-VIS spectrophotometry at 298 K. These compounds exhibited unexpectedly very low pK_a values in the range of 0–2 for amino derivatives and in the range of 7 for hydroxy derivatives. Electronic structure calculations by ab initio and DFT methods together with an X-ray measurement indicated that these results may be attributed to a markedly negative π charge on the carbon 5 together with a positive π charge on the basic substituent of the carbon 4. As a result, the dithiole nucleus exerts in this case a strong ─R effect. Although they were very low, pK _a values of 4-aminodithiolethiones remained still higher than those found with 5-aminodithiolethiones, which were also determined in this work for comparison. The latter were not unexpectedly in the range -3 < pH < ?2.     

Radical Ions in Photochemistry. 44. The Photo-NOCAS Reaction with Acetonitrile as the Nucleophile

Studies on the photoinduced electron transfer (PET) reactions of isobutylene (2-methylpropene, 1) in the absence of methanol have identified a new photochemical nucleophile-olefin combination, aromatic substitution (photo-NOCAS) reaction. Under these conditions acetonitrile was found to act as the nucleophile and to combine with the alkene radical cation. The resulting distonic radical cation then adds to the radical anion of 1,4-dicyanobenzene (2(-*)). The final product (6) results from cyclization into the ortho postion of the phenyl group. This product formation is rationalized on the basis of the relatively high oxidation potential of the alkene (i.e., one-electron oxidation yields a reactive radical cation), the fact that addition of the nucleophile (acetonitrile) to the radical cation is relatively unhindered, and the relatively low acidity of the radical cation due to the low radical stability of the allylic radical formed upon deprotonation. High-level ab initio molecular orbital calculations were used to determine the structures and relative energies of the possible intermediate distonic and bridged radical cations. The scope and mechanism of this type of photo-NOCAS reaction are discussed.     

苯分子离子的理论研究

由于 Jahn-Teller效应 [1]具有简并的最高占据分子轨道 ( HOMO)的分子失去一个电子生成阳离子后 ,构型将发生重大变化 .苯分子的构型为 D6 h点群 ,其简并的 HOMO用 e1g表示 ,从简并的 HOMO上失去一个电子后的苯分子离子将具有简并的电子态 2 E1g.根据 Jahn-Teller理论 ,苯分子离子将由 D6 h构型畸变为D2 h构型 ,同时简并的电子态将分裂为 2 B2 g和 2 B1g两个电子态 ,对应于 2个不同的 D2 h结构 .然而 Jahn-Teller理论既未说明 2 B2 g和 2 B1g态中哪个能量更低 ,也未说明 D2 h构型的细节 ,故需用量子化学计算来确定 .苯分子离子…     

Conformational study of 3β,16β-dihydroxyfriedelane by NMR and ab initio calculations

The complete chemical shift assignments of 3β,16β-dihydroxyfriedelane, a natural compound isolated from the hexane extract of Maytenus acanthophylla leaves was achieved through 1D/2D NMR spectral data. Combining ab initio Hartree-Fock [HF/6-31G(d)] and Density Functional Theory [DFT/B3LYP/6-31G(d,p)] calculations with NMR spectral data, it was possible to establish the predominance of the chair-chair-chair-boat-boat conformation for the five six-membered ring systems in this pentacyclic triterpene.     

Solution conformation of longifolene and its precursor by NMR and ab initio calculations

We describe the conformation and stereospecific 1H and 13C chemical shift assignments of longifolene 1 and its penultimate precursor 2 through the combined use of ab initio calculations and experimental NMR techniques. The predicted stable conformation for both compounds was similar and adopts a twisted chair conformation at the seven-membered ring where C4 lies on top of the exocyclic double bond. The calculated chemical shifts for the stable conformation agree well with the experimental values.     

Specific and nonspecific interactions in a molecule with flexible side chain: 2-phenylethanol and its 1:1 complex with argon studied by high-resolution UV spectroscopy

Using high-resolution resonance-enhanced two-photon ionization spectroscopy in combination with genetic-algorithm-based computer-aided rotational fit analysis and ab initio quantum chemistry calculations we determined the conformational structure and transition moment orientation in 2-phenylethanol and its 1:1 clusters with argon. The results clearly demonstrate that the gauche structure of 2-phenylethanol, which is stabilized by the intramolecular pi-hydrogen bond between the folded side chain and the benzene ring, is the most abundant in the cold molecular beam. In this conformer the transition moment is rotated by 18 degrees from the short axis of the aromatic ring. Two distinct 1:1 complexes of 2-phenylethanol with argon in a cis- and trans-configuration with respect to the side chain have been found. Employing the Kraitchman [Am. J. Phys. 21, 17 (1953)] analysis we have found that the structure of the 2-phenylethanol moiety and the orientation of the transition moment do not change after the complexation with argon within the experimental accuracy. From the measured band intensities we conclude that in addition to the dispersion interaction of the argon atom with the aromatic ring a hydrogen-bond-type interaction with the terminal -OH group of the side chain stabilizes the cis-structure of the 1:1 complex of 2-phenylethanol with argon.