Mesoionic tetrazolium-5-aminides: Synthesis, molecular and crystal structures, UV–vis spectra, and DFT calculations

• Vladislav A. Budevich,
• Sergei V. Voitekhovich,
• Alexander V. Zuraev,
• Vadim E. Matulis,
• Vitaly E. Matulis,
• Alexander S. Lyakhov,
• Ludmila S. Ivashkevich and
• Oleg A. Ivashkevich

Beilstein J. Org. Chem. 2021, 17, 385–395, doi:10.3762/bjoc.17.34

• recorded on a Bruker Vertex 70 spectrometer in diamond cell accessory. For Raman spectra registration, an Ocean Optics ID RAMAN READER (785 nm) spectrometer was used. Experimental procedures The experimental procedures are given in Supporting Information File 1. Computation details Calculations of the UV

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• nm. However, the fluorescence of these probes increases to a different extent upon addition of different 14-3-3 protein isoforms and the emission spectrum is blue-shifted to 530 nm (Figure 7B). Computation studies confirmed that enhancement of the fluorescence is due to close proximity of the

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• rotamers. By comparison, ΔH between the two rotamers was obtained experimentally by fitting the van ‘t Hoff equation to the population differences observed in the 19F NMR spectra between 224 and 264 K. 0.89 kcal⋅mol−1 is in tolerable agreement with the computation. Comparing 3a, 4a, 4b, and 6a in Table 2

A proposed sustainability index for synthesis plans based on input provenance and output fate: application to academic and industrial synthesis plans for vanillin as a case study

• John Andraos

Beilstein J. Org. Chem. 2020, 16, 2346–2362, doi:10.3762/bjoc.16.196

• of the target product that is actually used for its intended purpose. Renewable energy sources are defined as originating from hydroelectric, wind, solar, geothermal, and biomass sources. The computation of SI is illustrated for 22 synthesis plans of the high commodity flavour ingredient vanillin

• will end up wasted along supply chains and by end-of-use consumers. In order to facilitate computation of SI an Excel-based calculator was developed that can be used for any synthesis plan once all inputs and outputs are identified (see Supporting Information File 2). Firstly, for a given synthesis

• be made if full disclosure of both supply and disposal chains in the chemical enterprise exists. We note that this is a formidable challenge for the chemical community to accept and adopt in routine practice. We also note that the computation of SI will necessarily involve significant assumptions to

Design, synthesis and application of carbazole macrocycles in anion sensors

• Alo Rüütel,
• Ville Yrjänä,
• Sandip A. Kadam,
• Indrek Saar,
• Mihkel Ilisson,
• Astrid Darnell,
• Kristjan Haav,
• Tõiv Haljasorg,
• Lauri Toom,
• Johan Bobacka and
• Ivo Leito

Beilstein J. Org. Chem. 2020, 16, 1901–1914, doi:10.3762/bjoc.16.157

• studied anions. Additionally, for MC003, intramolecular hydrogen bonds could be present. For most anions, the champion molecules were MC007 and MC009. According to the computation results, neither benzoate nor pivalate were able to fit into the ring of these receptors because these anions were too large

Regioselectivity of glycosylation reactions of galactose acceptors: an experimental and theoretical study

• Enrique A. Del Vigo,
• Carlos A. Stortz and
• Carla Marino

Beilstein J. Org. Chem. 2019, 15, 2982–2989, doi:10.3762/bjoc.15.294

• functions describe better soft–soft interactions between nucleophiles and electrophiles [8][37][38]. The charge density was calculated for both methods using the Merz–Singh–Kollman scheme (MK) [39][40]. For the calculation of Fukui functions, besides the known computation of differences in atomic charges

Experimental and computational electrochemistry of quinazolinespirohexadienone molecular switches – differential electrochromic vs photochromic behavior

• Eric W. Webb,
• Jonathan P. Moerdyk,
• Kyndra B. Sluiter,
• Benjamin J. Pollock,
• Amy L. Speelman,
• Eugene J. Lynch,
• William F. Polik and
• Jason G. Gillmore

Beilstein J. Org. Chem. 2019, 15, 2473–2485, doi:10.3762/bjoc.15.240

• regiospecificity of photochromic vs electrochromic ring-opening of the QSHDs (Scheme 3) by experiment, we next sought to understand why SW would open differently upon excitation to SW* vs reduction to SW•−. We turned to computation (of 3a, 4a, and 5a) for an explanation. Due to large differences in the methods for

• calculating excited and ground-states, the triplet T0 state was used instead of the singlet S1 state as the photochemical intermediate (SW*) for computational purposes. Since T0 is the lowest energy triplet state, it is amenable to a ground-state computation. While the real SW* photochemical intermediate may

• length, bond order, and molecular orbitals to rationalize the observed differential photochromic and electrochromic ring-opening of 1 to 2 and 3, respectively, were performed on the Midwest Undergraduate Computation Chemistry Consortium (MU3C) cluster [28][29]. Computations were performed on a single

Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• ultrafine grid in the computation of two-electron integrals and their derivatives. The true minima were verified by performing frequency calculations in the corresponding environment. The TD-DFT method [27][28][29], carried out with the same functional and basis set, was used for predicting vertical

A diastereoselective approach to axially chiral biaryls via electrochemically enabled cyclization cascade

• Hong Yan,
• Zhong-Yi Mao,
• Zhong-Wei Hou,
• Jinshuai Song and
• Hai-Chao Xu

Beilstein J. Org. Chem. 2019, 15, 795–800, doi:10.3762/bjoc.15.76

• for the electrochemical synthesis of 3a. Computation investigation on the vinyl radical cyclization. DFT (M06-2X/6-31G*) calculated energetics (kcal mol−1) are Gibbs free energies in MeCN. Investigation on the effects of substituents on the diastereoselectivity.a Supporting Information Supporting

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• silicon surface without an intermediate that would show up as stationary point in the energy profile [5][6][7]. The only difference is found in the adsorption paths when dispersion corrections are included in the computation (Figure 3a).The curve is rather constantly shifted by 5–10 kJ·mol−1 towards more

• negative bonding energies Ebond in case of the precovered surface. This is not found in the computation that omits dispersion forces (Figure 3b). Thus, dispersion interactions not only stabilize product 3 but act along the whole adsorption path of 1 onto Si(001). This leads us to a comprehensive

• (stabilization by less than 5 kJ·mol−1) are found by including dispersion in the computation. If one molecule of 1 is already present at the surface, parts of the surface are inaccessible due to strong Pauli repulsion and overlapping molecules. This is indicated by the white areas around the first adsorbate in

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• similar with and without pair-wise interactions, is at ca. 8.1 THz for the dispersion-inclusive computation. THz vibrational frequencies, as a function of mode number, obtained for the orthorhombic (a) and monoclinic (b) polymorphs of TNT using the TS-vdW and MBD approaches. Comparison of computed

Conformational preferences of α-fluoroketones may influence their reactivity

• Graham Pattison

Beilstein J. Org. Chem. 2017, 13, 2915–2921, doi:10.3762/bjoc.13.284

• , supported by computation, that this effect is due to reactive conformations in which the C–X bond is orthogonal to the carbonyl group for good orbital overlap being disfavoured in the case of fluoro ketones. Keywords: α-halogenated ketones; conformational analysis; reactivity; stereoelectronic effects

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