A computational study of base-catalyzed reactions of cyclic 1,2-diones: cyclobutane-1,2-dione

• Nargis Sultana and
• Walter M. F. Fabian

Beilstein J. Org. Chem. 2013, 9, 594–601, doi:10.3762/bjoc.9.64

• variety of ab initio (MP2, SCS-MP2, CCSD(T), CEPA/1) and density functional (M06-2X) methods. Three possible reaction paths of the initially formed tetrahedral adduct leading to either 1-hydroxycyclopropane-1-carboxylate (benzilic acid type rearrangement, path A), α-oxobutanoate (path B) or γ-oxobutanoate

• reaction appears to be the formation of 1-hydroxycyclopropane-1-carboxylate, which is corroborated by previous experimental observations. Keywords: ab initio; density functional; reactive intermediate; rearrangement; ring opening; Introduction Addition of nucleophiles, e.g., OH–, to 1,2-dicarbonyl

• best of our knowledge no attempt has been made so far to consider the additional pathways B and C in these reactions. Here we present a detailed computational study (DFT and ab initio) of the base-catalyzed reactions of cyclobutane-1,2-dione (1) taking into account all three possible pathways. Results

Asymmetric Diels–Alder reaction with >C=P– functionality of the 2-phosphaindolizine-η¹-P-aluminium(O-menthoxy) dichloride complex: experimental and theoretical results

• Rajendra K. Jangid,
• Nidhi Sogani,
• Neelima Gupta,
• Raj K. Bansal,
• Moritz von Hopffgarten and
• Gernot Frenking

Beilstein J. Org. Chem. 2013, 9, 392–400, doi:10.3762/bjoc.9.40

• (endo) and TS2 (exo) and the products 8a and 8a’, respectively. On the other hand, attack of the diene from the sterically hindered Re face leads to the transition structure TS3 and the product 10. Energetics Ab initio investigations of the DA reaction of phosphaethene with 2H-phosphole [49] and with

Inclusion of the insecticide fenitrothion in dimethylated-β-cyclodextrin: unusual guest disorder in the solid state and efficient retardation of the hydrolysis rate of the complexed guest in alkaline solution

• Dyanne L. Cruickshank,
• Natalia M. Rougier,
• Raquel V. Vico,
• Susan A. Bourne,
• Elba I. Buján,
• Mino R. Caira and
• Rita H. de Rossi

Beilstein J. Org. Chem. 2013, 9, 106–117, doi:10.3762/bjoc.9.14

• in the Cambridge Crystallographic Database [15], which necessitated its ab initio structural solution by using direct methods. Density considerations indicated an asymmetric unit containing two complex molecules. In addition, prior to structural solution, a special feature was evident from the X-ray

• possible to deduce the presence of two DIMEB molecules in the asymmetric unit. As no isostructural DIMEB complex could be found in the literature, the program SHELXD [27] was employed to solve the structure by ab initio direct methods. The initial structural solution (correlation coefficient = 84.9

Theoretical study on β-cyclodextrin inclusion complexes with propiconazole and protonated propiconazole

• Adrian Fifere,
• Narcisa Marangoci,
• Stelian Maier,
• Adina Coroaba,
• Dan Maftei and
• Mariana Pinteala

Beilstein J. Org. Chem. 2012, 8, 2191–2201, doi:10.3762/bjoc.8.247

• theoretical study of their supramolecular associates. Accurately representing the size of CD cavities and their chain flexibility represents a challenge for molecular simulation when quantum methods are employed. Since the ab initio approach is time consuming for this kind of molecule, quantum semi-empirical

• geometry optimization, due to its improved description of hydrogen bonds and steric effects [8][9][10]. Advanced methods, such as Hartree–Fock (HF) and density functional theory (DFT), were also applied in cyclodextrin chemistry to explain experimental data [11][12]. Very often, ab initio methods are used

Synthesis and evaluation of new guanidine-thiourea organocatalyst for the nitro-Michael reaction: Theoretical studies on mechanism and enantioselectivity

• Tatyana E. Shubina,
• Matthias Freund,
• Sebastian Schenker,
• Timothy Clark and
• Svetlana B. Tsogoeva

Beilstein J. Org. Chem. 2012, 8, 1485–1498, doi:10.3762/bjoc.8.168

• . Extensive DFT calculations, including solvent effects and dispersion corrections, as well as ab initio calculations provide a plausible description of the reaction mechanism. Keywords: bifunctional organocatalyst; DFT calculations; guanidine-thiourea; Michael addition; organocatalysis; transition states

Cation affinity numbers of Lewis bases

• Christoph Lindner,
• Raman Tandon,
• Boris Maryasin,
• Evgeny Larionov and
• Hendrik Zipse

Beilstein J. Org. Chem. 2012, 8, 1406–1442, doi:10.3762/bjoc.8.163

• substrate model for acyl-transfer reactions. Affinities towards these cationic electrophiles are complemented by data for Lewis-base addition to Michael acceptors as prototypical neutral electrophiles. Keywords: ab initio; cation affinity; Lewis basicity; organocatalysis; proton affinity; Introduction

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• molecular motion similar to a hinge, in which the two aromatic rings are arranged at an angle of 90°. The photoisomerization process involves three isomeric forms: (trans,trans), (trans,cis) and (cis,cis). The heats of formation of the three isomers were determined by ab initio quantum chemical calculations

Enantioselective supramolecular devices in the gas phase. Resorcin[4]arene as a model system

• Caterina Fraschetti,
• Matthias C. Letzel,
• Antonello Filippi,
• Maurizio Speranza and
• Jochen Mattay

Beilstein J. Org. Chem. 2012, 8, 539–550, doi:10.3762/bjoc.8.62

• by several computational supports (molecular dynamics and ab initio optimization). The dynamic point of view is fundamental for supramolecular ionic aggregates, because the synergy of several noncovalent interactions confers a pronounced stability even to very flexible aggregates, and the lifetime of

Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides

• Kenichirou Yokota,
• Masayori Hagimori,
• Naoko Mizuyama,
• Yasuhisa Nishimura,
• Hiroshi Fujito,
• Yasuhiro Shigemitsu and
• Yoshinori Tominaga

Beilstein J. Org. Chem. 2012, 8, 266–274, doi:10.3762/bjoc.8.28

• reproduced by a series of ab initio quantum-chemical calculations. Keywords: amino group; fluorescence; HOMO/LUMO; pyrimidine; solid-state; Introduction Solid-state fluorescent compounds are currently attracting considerable interest from both theoretical and practical standpoints [1][2][3][4]. Recently

• pyrimidine derivatives. It is thought that these derivatives show strong fluorescence as a result of the presence of a hetero-π-electron conjugated system [7]. The electronic and emission spectra of these new compounds were analyzed computationally by using a series of ab initio quantum-chemical calculations

• carried out ab initio molecular-orbital calculations, focused on 3a (Figure 3). The computed key bond lengths are shown in Table 3. Comparison of the S0 (DFT) and S1 (CIS) bond lengths shows that the S0→S1 (dominant HOMO→LUMO) transition is reflected in the bond-length variations. The C4–C5 bond, with a

Imidazole as a parent π-conjugated backbone in charge-transfer chromophores

• Jiří Kulhánek and
• Filip Bureš

Beilstein J. Org. Chem. 2012, 8, 25–49, doi:10.3762/bjoc.8.4

• -A-π-D and D-π-A-π-A systems. The performed ab initio and INDO/S MO calculations of ground-state dipole moments and first-order hyperpolarizabilities β revealed that the latter chromophore arrangement resulted in significantly enhanced nonlinearities. The benzimidazolate anion as a donor moiety was

NMR studies of anion-induced conformational changes in diindolylureas and diindolylthioureas

• Damjan Makuc,
• Jennifer R. Hiscock,
• Mark E. Light,
• Philip A. Gale and
• Janez Plavec

Beilstein J. Org. Chem. 2011, 7, 1205–1214, doi:10.3762/bjoc.7.140

• along the C7–N7α bonds and the syn–syn conformer was preferred for anion–receptor complexes. The conformational changes upon anion binding are in good agreement with energetic preferences established by ab initio calculations. Keywords: anion recognition; conformation analysis; host–guest systems; NMR

• -anions, were studied by NMR spectroscopy and supported by energetic preferences established from ab initio calculations. Results and Discussion Synthesis Compounds 1–3 were synthesized following a previously reported methodology [36][37][38][39]. Compound 4 was prepared by reaction of 7-amino-N-phenyl-1H

• . Furthermore, binding of anions caused conformational changes along the C7–N7α bonds, and the syn–syn conformer was predominant in the anion–receptor complexes according to both NOE enhancements and ab initio calculations in solution. The freely optimized syn–syn conformer of the 1·AcO− complex retained a

Alkene selenenylation: A comprehensive analysis of relative reactivities, stereochemistry and asymmetric induction, and their comparisons with sulfenylation

• Vadim A. Soloshonok and
• Donna J. Nelson

Beilstein J. Org. Chem. 2011, 7, 744–758, doi:10.3762/bjoc.7.85

• directly bonded to the C=C are included in this study to avoid undesirable complicating effects associated with ring strain, polarization, or conjugation [72][73][74][75][76][77][78]. Experimental IEs for alkenes in Table 1 are used as reported in the literature [79]. Alkene ab initio (HF level, 6-31G

• different methods are shown in the Supporting Information File 1. Four computational methods, including an ab initio method at HF level in five different basis sets (3-21G(*), 6-31G*, 6-31+G*, 6-311G*, and 6-311+G*), two semi-empirical methods (PM3 and MNDO), and a DFT method (B3LYP/6-31G*), were used to

Molecular rearrangements of superelectrophiles

• Douglas A. Klumpp

Beilstein J. Org. Chem. 2011, 7, 346–363, doi:10.3762/bjoc.7.45

• (87) which was found to be stable at −105 °C. However, upon warming to −60 °C, the 3,7-dimethylbicyclo[3.3.1]nona-3,7-diyl dication (88) was formed. This isomerization is thought to occur through a series of hydride shifts, Wagner–Meerwein shifts, ring contractions, and methyl shifts (Scheme 18). Ab

• initio calculations were performed and revealed that the isomerization lowers the energy of the dication by about 26 kcal/mol. Moreover, isomerization increased the distance between the carbocation sites from 2.80 Å in 87 to 3.58 Å in 88. Olah and coworkers have described [30] an attempt to generate the

Accuracy in determining interproton distances using Nuclear Overhauser Effect data from a flexible molecule

• Catharine R. Jones,
• Craig P. Butts and
• Jeremy N. Harvey

Beilstein J. Org. Chem. 2011, 7, 145–150, doi:10.3762/bjoc.7.20

• 0.03, 0.00, 0.20 and 0.14 kJ/mol, very close to the coupled-cluster values, suggesting that these quantities are reliable to ± 0.5 kJ/mol and perhaps better. Including the corrections for zero-point energy, thermal and entropic corrections, and solvation, these correlated ab initio calculations lead to

Catalysis: transition-state molecular recognition?

• Ian H. Williams

Beilstein J. Org. Chem. 2010, 6, 1026–1034, doi:10.3762/bjoc.6.117

• importance for enzyme catalysis of destabilisation as well as binding has also been noted by Jencks [14]. Some years ago I performed an ab initio Hartree–Fock investigation [15], intended to test the validity of the compression hypothesis; this exercise amounted to the computational design of a catalyst for

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• from Kebarle et al. who showed that binding of potassium ions to benzene and water in the gas phase is of similar energy [9][12]. Ammonium–π-interactions were experimentally investigated in detail as well as by ab initio calculations and are mainly based on electrostatic interactions. The binding

An enantiomerically pure siderophore type ligand for the diastereoselective 1 : 1 complexation of lanthanide(III) ions

• Markus Albrecht,
• Olga Osetska,
• Thomas Abel,
• Gebhard Haberhauer and
• Eva Ziegler

Beilstein J. Org. Chem. 2009, 5, No. 78, doi:10.3762/bjoc.5.78

• following the absorption at 279 nm. Analysis of the titration data reveals high binding constants for lanthanum(III) (Ka = 8.3 × 105 M−1) as well as europium(III) (Ka = 7.8 × 105 M−1) for the reaction of deprotonated ligand 1a3− with the Ln3+ ion to form [(1a)Ln] in methanol at room temperature. Ab initio

• calculations In order to determine the configuration at the metal centres of the 1a·Ln (R = Et) complexes ab initio calculations were performed for the stereoisomers of complex 1b·La (R = Me) [37]. The difference between 1a and 1b is only the substitution of the ethyl groups in 1a by methyl groups in 1b. This

• ) ions, while smaller cations lead to an unspecific complex formation (probably oligomerization or polymerization). On the basis of ab initio calculations and CD spectroscopy we could show that the formed complex (1a)La exhibits exclusively Λ helicity. We were able to isolate the corresponding lanthanum

Influence of spacer chain lengths and polar terminal groups on the mesomorphic properties of tethered 5-phenylpyrimidines

• Gundula F. Starkulla,
• Elisabeth Kapatsina,
• Angelika Baro,
• Frank Giesselmann,
• Stefan Tussetschläger,
• Martin Kaller and
• Sabine Laschat

Beilstein J. Org. Chem. 2009, 5, No. 63, doi:10.3762/bjoc.5.63

• are possible, i.e. 4-, 5-, and 2-phenylpyrimidine, only the latter two are suitable for liquid crystals. Furthermore 5- and 2-phenylpyrimidines differ in their overall conformation. According to ab initio calculation by Barone [2], 2-phenylpyrimidine is almost planar, whereas 5-phenylpyrimidine has a

The role of an aromatic group in remote chiral induction during conjugate addition of α-sulfonylallylic carbanions to ethyl crotonate

• Shlomo Levinger,
• Ranjeet Nair and
• Alfred Hassner

Beilstein J. Org. Chem. 2008, 4, No. 32, doi:10.3762/bjoc.4.32

• geometry of the aromatic ring during chelation with the lithiated species is as yet unknown, it evidently plays an important role in determining the approach of the carbanion to the conjugate acceptor and thus the stereoselectivity of the conjugate addition. Preliminary ab initio calculations [17] for the

• yields are obtained with aromatic rings possessing higher electron density (4-methoxyphenyl, 2-thienyl) while the employment of the 9-anthryl nucleus results in complete transmission of chirality to the newly formed stereogenic centers. Ab initio calculations assign an important role to Li+–aromatic π

Reactions of glycidyl derivatives with ambident nucleophiles; part 2: amino acid derivatives

• Gerald Dyker,
• Andreas Thöne and
• Gerald Henkel

Beilstein J. Org. Chem. 2007, 3, No. 28, doi:10.1186/1860-5397-3-28

• from a weak intramolecular hydrogen bond. According to ab initio calculations for cis-9a, (B3LYP, 6-31G*, zero point energy included) this structure is indeed 1.9 kcal/mol more stable than its exo-oriented conformer and 2.2 kcal/mol more stable than its trans-stereoisomer. Conclusion In summary, we

The vicinal difluoro motif: The synthesis and conformation of erythro- and threo- diastereoisomers of 1,2-difluorodiphenylethanes, 2,3-difluorosuccinic acids and their derivatives

• David O'Hagan,
• Henry S. Rzepa,
• Martin Schüler and
• Alexandra M. Z. Slawin

Beilstein J. Org. Chem. 2006, 2, No. 19, doi:10.1186/1860-5397-2-19

• erythro- and threo- 2,3-difluorosuccinic acids were then prepared. The solid and solution state conformation of these compounds was assessed by X-ray crystallography and NMR. Ab initio calculations were also carried out to model the conformation of erythro- and threo- 1,2-difluoro-1,2-diphenylethane as

• suggests that the fluorine gauche effect is over-riding any steric repulsion between the phenyl rings. To explore the significance of these solid state conformations further, NMR solution studies and ab initio analysis, exploring the preferred conformations for each of the diastereoisomers was carried out

• ). Conformational energy calculations on erythro and threo-13 Due to the ambiguous solution state study particularly for erythro-13, ab initio calculations were carried out at the B3LYP//cc-pVTZ level exploring absolute energies of the three staggered conformers of both erythro- and threo- 13 [24][25]. The