A permutation approach to the assignment of the configuration to diastereomeric tetrads by comparison of experimental and ab initio calculated differences in NMR data

• Przemysław J. Boratyński

Beilstein J. Org. Chem. 2017, 13, 2478–2485, doi:10.3762/bjoc.13.245

• computation has been applied for comparison of diastereomers against a universal database made of known compounds [11][12]. Results and Discussion The idea presented herein is to rank all possible permutations of experimental and computed data rather than focusing on individual pairs. The tetrads need to

Base-promoted isomerization of CF₃-containing allylic alcohols to the corresponding saturated ketones under metal-free conditions

• Yoko Hamada,
• Tomoko Kawasaki-Takasuka and
• Takashi Yamazaki

Beilstein J. Org. Chem. 2017, 13, 1507–1512, doi:10.3762/bjoc.13.149

• the toluene refluxing temperature, and utilization of the corresponding optically active substrates unambiguously demonstrated that this transformation proceeded in a highly stereoselective fashion. Keywords: allylic alcohols; chirality; computation; 1,3-proton shift; trifluoromethyl; Introduction

• this interesting and efficient protocol, computation was performed [7] for obtaining the rough indication of the acidity of both protons Ha and Hb in 1F. Moreover, the corresponding allylic alcohols 2F as well as their non-fluorinated counterparts 1H and 2H were also employed for comparison whose

• present instance to afford the desired compound 7a in 67% isolated yield (Table 2, entry 2). The result that the stronger tertiary amine DBU worked more effectively than Et3N was a clear support of our computation at least from a qualitative point of view which estimated the lower acidity of the allylic

Biomimetic molecular design tools that learn, evolve, and adapt

• David A Winkler

Beilstein J. Org. Chem. 2017, 13, 1288–1302, doi:10.3762/bjoc.13.125

• layer nodes where nonlinear computation is performed. The inputs to each hidden layer node are summed and transformed by a nonlinear transfer function in the hidden layer node. The output of these nodes is transmitted to the output layer node (there can be more than one) where the weights are summed and

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• series [4] to better extract meaning from their measured properties. I came to appreciate a healthy mix of computation, synthesis and characterization, and I endeavor to use that approach every day. Yet, in spite of all the careful planning, I also learned the importance of simply trying it, or as Keith

Solving the puzzling competition of the thermal C²–C⁶ vs Myers–Saito cyclization of enyne-carbodiimides

• Anup Rana,
• Mehmet Emin Cinar,
• Debabrata Samanta and
• Michael Schmittel

Beilstein J. Org. Chem. 2016, 12, 43–49, doi:10.3762/bjoc.12.6

• pathway if the trapping reaction by hydrogen transfer is no more rate determining. Keywords: DFT computation; diradical; enyne-carbodiimides; hydrogen transfer; thermal cyclization; Introduction The thermal cyclizations of enediynes [1][2][3][4][5][6], enediallenes [7][8][9][10], bisallenes [11], enyne

• approach for the diradical species and the transition states (TSs) connecting them while the restricted method was used for closed shell species. The BLYP functional was chosen for computation because the benchmark studies done by Schreiner showed good applicability of BLYP for the enyne-allene system [3

Bright molecules for sensing, computing and imaging: a tale of two once-troubled cities

• A. Prasanna de Silva

Beilstein J. Org. Chem. 2015, 11, 2774–2784, doi:10.3762/bjoc.11.298

• electron transfer) sensing/switching as a design tool, b) the construction of a market-leading blood electrolyte analyzer and c) the invention of molecular logic-based computation as an experimental field, are delineated. Efforts to extend the philosophy of these approaches into issues of small object

• identification, nanometric mapping, animal visual perception and visual art are also outlined. Keywords: blood electrolyte analyzer; luminescent PET sensing/switching; molecular logic-based computation; photoinduced electron transfer; small molecular edge detection; Review Prologue Colombo, Sri Lanka: A civil

• possible information processors [56]. Then it dawned on me that the 'lumophore–spacer–receptor’ system could be elaborated into Boolean logic devices with chemical inputs and luminescence output. The first device, which initiated molecular logic-based computation as an experimental field, arose in the form

Computational study of productive and non-productive cycles in fluoroalkene metathesis

• Markéta Rybáčková,
• Jan Hošek,
• Ondřej Šimůnek,
• Viola Kolaříková and
• Jaroslav Kvíčala

Beilstein J. Org. Chem. 2015, 11, 2150–2157, doi:10.3762/bjoc.11.232

• . Keywords: alkene metathesis; computation; DFT; fluoroalkene; mechanism; non-productive cycle; productive cycle; Introduction Over the course of the last 20 years, alkene metathesis catalysed with homogeneous transitition metal-based precatalysts evolved into a valuable tool for organic synthetic chemists

• continued our study by the computation of the first step A of the catalytic cycle for 1,1-difluoroethene (2), which started with the coordination of the starting active catalytic form 2AC with 1,1-difluoroethene (2). The non-productive cycle started with the syn-coordination of 1,1-difluoroethene (2) to 1,1

Why base-catalyzed isomerization of N-propargyl amides yields mostly allenamides rather than ynamides

• Armando Navarro-Vázquez

Beilstein J. Org. Chem. 2015, 11, 1441–1446, doi:10.3762/bjoc.11.156

• requires a very high level of theory [9], and expensive CCSD(T)/cc-pVQZ//MP2/cc-pVTZ coupled cluster computations were needed to match the experimental propadiene to propyne isomerization energy of −1.4 kcal/mol [10]. In order to choose a standard test methodology for the computation of allenamide–ynamide

• fixed as s-E. This CBS-QB3 method furnished a ΔH0 energy of −0.8 kcal/mol for propadiene to propyne isomerization, which is somewhat lower than the reported experimental energy. Note, however, that the result is close to that furnished by the much more computationally expensive W1 [13] computation on

• of the involved species. Simple allenamides or allencarbamates are in general more stable than the corresponding N-alkynyl isomers but the sign of the small energy gap can be reversed through structural changes. The ωB97 functional gave reasonable performance for the computation of isomerization

On the strong difference in reactivity of acyclic and cyclic diazodiketones with thioketones: experimental results and quantum-chemical interpretation

• Andrey S. Mereshchenko,
• Alexey V. Ivanov,
• Viktor I. Baranovskii,
• Grzegorz Mloston,
• Ludmila L. Rodina and
• Valerij A. Nikolaev

Beilstein J. Org. Chem. 2015, 11, 504–513, doi:10.3762/bjoc.11.57

• energy for the 1,5-electrocyclization (ΔG1#) is usually smaller than for the 1,3-electrocyclization (ΔG2#). The obtained computation results are in good agreement with the experimental observations, which demonstrate that at 20 °C, due to a kinetic reaction control, 1,3-oxathioles 3 and 3’ are in most

Aspergiloid I, an unprecedented spirolactone norditerpenoid from the plant-derived endophytic fungus Aspergillus sp. YXf3

• Zhi Kai Guo,
• Rong Wang,
• Wei Huang,
• Xiao Nian Li,
• Rong Jiang,
• Ren Xiang Tan and
• Hui Ming Ge

Beilstein J. Org. Chem. 2014, 10, 2677–2682, doi:10.3762/bjoc.10.282

• ], and refined anisotropically by full-matrix least-squares on F2 using SHELXL-97. The absolute configurations were determined by computation of the Hooft parameter [13], in all cases yielding a probability of 1.000 that the reported configuration is correct. Crystal data: C18H26O4, M = 306.39

The Ugi four-component reaction as a concise modular synthetic tool for photo-induced electron transfer donor-anthraquinone dyads

• Sarah Bay,
• Gamall Makhloufi,
• Christoph Janiak and
• Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 1006–1016, doi:10.3762/bjoc.10.100

• density of the HOMO is almost completely localized on the phenothiazine unit whereas the coefficient density of the LUMO resides on the anthraquinone core, supporting the electronic decoupling of the donor and the acceptor in the electronic ground state. In conclusion the computation underlines that in

Tailoring of organic dyes with oxidoreductive compounds to obtain photocyclic radical generator systems exhibiting photocatalytic behavior

• Christian Ley,
• Julien Christmann,
• Ahmad Ibrahim,
• Luciano H. Di Stefano and
• Xavier Allonas

Beilstein J. Org. Chem. 2014, 10, 936–947, doi:10.3762/bjoc.10.92

• kinetics occuring in so called photocatalytic systems. The simple kinetic model used is enough to outline the benefit of the cyclic system and to give the basic requirements in term of chemical combination needed to be fulfilled in order to obtain a photocatalytic behavior. Keywords: computation; electron

• II PIS will be given and compared with a PCIS. Then, in order to improve the knowledge of PCIS, a thermodynamic and mechanistic approach of PCIS exhibiting an ideal photocatalytic behavior will be presented. The proposed scheme will be used as model to run some computation. This will permit to

• tuned to 9 mW/cm2 intensity. This will correspond to the 9 mW/cm3 computation condition (vide infra). The initial concentration was [RB]0 = 6.5 10−5 mol·L−1 (with ε = 31900 M−1·cm−1 and a length of l = 1 cm, this corresponds to an initial absorbance of around 0.2 at 532 nm) and [TA]0 = 10−3 mol·L−1. The

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

• Helge Klare,
• Jörg M. Neudörfl and
• Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

• interaction between the proton donors and the proton-accepting nitro group, two bonding patterns are possible that involve either one or both oxygen atoms of the nitro moiety. Computation of either conformation revealed both oxygen atoms acting as proton acceptors to be most favored with all motifs. This is

Regioselective carbon–carbon bond formation of 5,5,5-trifluoro-1-phenylpent-3-en-1-yne

• Motoki Naka,
• Tomoko Kawasaki-Takasuka and
• Takashi Yamazaki

Beilstein J. Org. Chem. 2013, 9, 2182–2188, doi:10.3762/bjoc.9.256

• electrophiles, under equilibration of the possible two anionic species. Keywords: additives; computation; Li···F chelation; deprotonation; electron-withdrawing effect; organo-fluorine; Introduction We have previously reported [1] the interesting behavior of (E)-1-chloro-3,3,3-trifluoropropene ((E)-1) [2][3][4

•  2, aldehydes preferentially yielded 5 with qualitatively better ratio of 5/6 than the one of 4-d1/4-d2. Our computation of 4-Li1 and 4-Li2 by Gaussian 09W [20] using the B3LYP/6-31+G* level of theory uncovered that the former was energetically more favorable than the latter by 5.34 (3.67) kcal/mol

Topochemical control of the photodimerization of aromatic compounds by γ-cyclodextrin thioethers in aqueous solution

• Hai Ming Wang and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1858–1866, doi:10.3762/bjoc.9.217

• mechanical calculations of the structures and interaction energies ΔE of the four COU dimers were performed using the Gaussian 03 software package to investigate the favored packing [47]. The aromatic dimers were fully optimized at the MP2/6-31G* level without any symmetry restriction during the computation

New tridecapeptides of the theonellapeptolide family from the Indonesian sponge Theonella swinhoei

• Annamaria Sinisi,
• Barbara Calcinai,
• Carlo Cerrano,
• Henny A. Dien,
• Angela Zampella,
• Claudio D’Amore,
• Barbara Renga,
• Stefano Fiorucci and
• Orazio Taglialatela-Scafati

Beilstein J. Org. Chem. 2013, 9, 1643–1651, doi:10.3762/bjoc.9.188

• able to significantly reduce the proliferation at 1 μM. At this dose, the proliferation reduction was equal to 20% (Figure 4, panel A; * p < 0.05 compared to untreated cells; n = 4). Computation of 50% inhibitory drug concentration (IC50) revealed that compounds 1, 2 and 3 were characterized by very

• mean ± standard error. Right panel: Computation of IC50 values. From top to bottom: Theonellapeptolide Id, sulfinyltheonellapeptolide and theonellapeptolide If (* p < 0.05 compared to untreated cells; n = 4). 1H (500 MHz) and 13C (125 MHz) NMR data of sulfinyltheonellapeptolide in CD3OD (2). 1H (500

Computational study of the rate constants and free energies of intramolecular radical addition to substituted anilines

• Andreas Gansäuer,
• Meriam Seddiqzai,
• Tobias Dahmen,
• Rebecca Sure and
• Stefan Grimme

Beilstein J. Org. Chem. 2013, 9, 1620–1629, doi:10.3762/bjoc.9.185

• systems. Kohn–Sham density functional theory (KS-DFT) has been proven to yield good accurate thermochemical properties within acceptable computation times [23][24][25]. However, the number of the proposed approximate exchange–correlation functionals to choose from is huge and they can suffer from severe

Host–guest complexes of mixed glycol-bipyridine cryptands: prediction of ion selectivity by quantum chemical calculations, part V

• Svetlana Begel,
• Ralph Puchta and
• Rudi van Eldik

Beilstein J. Org. Chem. 2013, 9, 1252–1268, doi:10.3762/bjoc.9.142

• structures were characterized as minima, transition structures, etc., by computation of vibrational frequencies. The relative energies were corrected for zero-point vibrational energies (ZPE). We deliberately did not include any solvent model for the sake of comparability with earlier studies [1][2][3][4

Tandem dinucleophilic cyclization of cyclohexane-1,3-diones with pyridinium salts

• Mostafa Kiamehr,
• Firouz Matloubi Moghaddam,
• Satenik Mkrtchyan,
• Volodymyr Semeniuchenko,
• Linda Supe,
• Alexander Villinger,
• Peter Langer and
• Viktor O. Iaroshenko

Beilstein J. Org. Chem. 2013, 9, 1119–1126, doi:10.3762/bjoc.9.124

• + regioselective reaction is inherent. Intrigued by this discrepancy, we computed the full reaction mechanism for cation 2a+ with potassium 3-oxocyclohex-1-enolate in the presence of potassium cation and hydrogencarbonate anion as base. We included HCO3− in our computation, both because it has only five atoms and

• the last reaction is a protonation of enamine in essence; the imaginary frequency inherent for TS 22a shows only proton displacement, without formation of a C–O bond. The latter was formed during IRC computation, starting from TS 22a. Previously, Hui Li and Chao-Guo Yan [50] proposed the nucleophilic

• scaling factor (0.9608) was applied. For every located transition state an IRC calculation at the same level of theory confirmed that this TS connects the corresponding educts/intermediates/products. The methodology of local softness computation [59][60] uses Fukui functions; for their approximation we

Interplay of ortho- with spiro-cyclisation during iminyl radical closures onto arenes and heteroarenes

• Roy T. McBurney and
• John C. Walton

Beilstein J. Org. Chem. 2013, 9, 1083–1092, doi:10.3762/bjoc.9.120

• computation [38] that gave hfs in close agreement with experiment (Table 1). This was a surprising result because previously the only radicals of type 9 that had been spectroscopically detected had resulted from additions of phenyl [34] or bridgehead radicals (bicyclo[2.2.2]oct-1-yl and adamantyl) [39]. These

• resolved spectra only at 230–235 K (Figure 3). The corresponding benzofuranyl-iminyl was not detectable at 230 K or above. The EPR hfs obtained from simulation of the spectrum (Table 2) show this to be a benzyl type radical and we assign it structure 12a (Scheme 2). A DFT computation for 12a at the UB3LYP

Ring opening of 2-aza-3-borabicyclo[2.2.0]hex-5-ene, the Dewar form of 1,2-dihydro-1,2-azaborine: stepwise versus concerted mechanisms

• Holger F. Bettinger and
• Otto Hauler

Beilstein J. Org. Chem. 2013, 9, 761–766, doi:10.3762/bjoc.9.86

• have performed explorative computations using the CASSCF(6,6)/6-31G* method and could locate transition states for the conrotatory (TS1; nimag = 1, i556 cm−1) and disrotatory (TS2; nimag = 1, i628 cm−1) ring opening of 3. Computation of the intrinsic reaction coordinates confirms that both TS1 and TS2

• -dihydro-1,2-azaborine system, while the four π and π* orbitals along with the C3–C6 σ/σ* orbitals were used for the Dewar form 3 and transition states TS1 and TS2. Geometries were fully optimised and the nature of stationary points was confirmed by analytic computation of second derivatives. Intrinsic

Electron and hydrogen self-exchange of free radicals of sterically hindered tertiary aliphatic amines investigated by photo-CIDNP

• Martin Goez,
• Isabell Frisch and
• Ingo Sartorius

Beilstein J. Org. Chem. 2013, 9, 437–446, doi:10.3762/bjoc.9.46

• this uncertainty, an elaborate computation of λi is not justified, but the calculated activation parameter is seen to be in very good agreement with the experimental result of Table 2. Finally, the slightly smaller molecular size of DABCO (d1 = d2 = 6.2 Å; d = 5.7 Å) leads to a computed increase of

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

• alkene IEs and required reasonable computation time. Although this computational method may not give absolute HOMO energy values, it was successfully used in similar, previous studies [72][73][74][75][76][77][78], and it was proven to be sufficiently accurate in correlations with IEs and the relative

EPR and pulsed ENDOR study of intermediates from reactions of aromatic azides with group 13 metal trichlorides

• Giorgio Bencivenni,
• Riccardo Cesari,
• Daniele Nanni,
• Hassane El Mkami and
• John C. Walton

Beilstein J. Org. Chem. 2010, 6, 713–725, doi:10.3762/bjoc.6.84

• +•, containing a single F-atom. The DFT computation on the dimer hfs gave satisfactory agreement (Table 1), with the possible exception of the para-F hfs. However, DFT-computed a(F) values varied from 7.2, to 7.1, to 9.5 and 4.3 G with 6-31G(d), 6-31+G(d,p), DGDZVP and 6-311++G(d,p) basis sets, respectively

Prediction of reduction potentials from calculated electron affinities for metal-salen compounds

• Sarah B. Bateni,
• Kellie R. England,
• Anthony T. Galatti,
• Handeep Kaur,
• Victor A. Mendiola,
• Alexander R. Mitchell,
• Michael H. Vu,
• Benjamin F. Gherman and
• James A. Miranda

Beilstein J. Org. Chem. 2009, 5, No. 82, doi:10.3762/bjoc.5.82

• predict reduction potentials, we hoped to establish a method of assessing the suitability of prospective metal-salen catalysts other than Ni(II)-salen as electrocatalysts in the ERC reaction. The indirect computation of reduction potentials in this manner avoids the need to compute solvation enthalpies

• (Epc) of the 19 metal-salens were then measured experimentally using cyclic voltammetry. Analogous methods were applied to obtain the Epc for a test set of 14 metal-salens employing a variety of new metals and substituents. Concurrently, density functional theory calculations enabled computation of EAs