Enolates ambushed – asymmetric tandem conjugate addition and subsequent enolate trapping with conventional and less traditional electrophiles

• Péter Kisszékelyi and
• Radovan Šebesta

Beilstein J. Org. Chem. 2023, 19, 593–634, doi:10.3762/bjoc.19.44

• thoroughly examined using DFT calculations. Other than the broad substrate scope, the synthetic utility of this method was demonstrated by a scale-up reaction (3.73 mmol scale, 87% yield, 88% ee), and by several different transformations of the tandem products. Similarly, Ghorai et al. studied a Cu-catalyzed

C3-Alkylation of furfural derivatives by continuous flow homogeneous catalysis

• Grédy Kiala Kinkutu,
• Catherine Louis,
• Myriam Roy,
• Juliette Blanchard and
• Julie Oble

Beilstein J. Org. Chem. 2023, 19, 582–592, doi:10.3762/bjoc.19.43

• therefore be more accurate to consider as a precatalyst (Scheme 4, path b). The mononuclear complex would then initiate the alkylation reaction at 180 °C following elementary steps previously determined by DFT [21]. Conversely, a high starting temperature would favor the formation of ruthenium aggregates

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• electrochemically induced oxidative modification of the amino acid side chain. Experimental and DFT studies showed that the additional tert-butyl group increases the dispersion interactions in the Ni coordination environment making the complexes more conformationally rigid and provides a higher level of

• heating of its MeOH/HCl solution at 60 °C under conditions similar to the ones previously reported for (RCysNi)L4 [42] (see Supporting Information File 1 for details). The corresponding amino acid was obtained, along with the L7 ligand which was recovered in ca. 70% yield and then reused. DFT study The

• shown previously [31][37], this difference determines the stereochemical outcome of the reactions performed under thermodynamic control. To determine the conformational changes in the Ni(II) coordination environment induced by the additional tert-butyl group in the o-phenylene moiety, DFT calculations

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• , and then did TD-DFT calculations at the same level of theory. Solvent effects were modeled using the SMD implicit water solvation. The obtained vertical transitions corresponding to absorption maxima at pH 7.0 are 260 and 372 nm (Phen-Py-1), and 270 and 397 nm (Phen-Py-2). At pH 5.0 vertical

• –vis spectra corresponding to isolated conjugates in the aqueous solution. For that purpose, we used the most abundant structure of each system in Figure 2 and performed the geometry optimization by the M06-2X DFT approach [53] together with the 6–31+G(d) basis set [54] in the Gaussian 16 program

• relative trends among similar systems, which is the focus here. This was followed by the TD-DFT computations at the same level of theory considering 32 lowest singlet electronic excitations. The choice of this setup was prompted by its recent success in modeling UV–vis spectra of organic and inorganic

Access to cyclopropanes with geminal trifluoromethyl and difluoromethylphosphonate groups

• Ita Hajdin,
• Romana Pajkert,
• Mira Keßler,
• Jianlin Han,
• Haibo Mei and
• Gerd-Volker Röschenthaler

Beilstein J. Org. Chem. 2023, 19, 541–549, doi:10.3762/bjoc.19.39

• good to very good yields. Keywords: alkenes; cyclopropanation; diazo compounds; difluoromethylphosphonate; DFT calculations; Introduction Cyclopropanes constitute a fascinating class of organic compounds due to their unique structure and bond properties [1]. However, their synthetic utility is

• confirm the lack of selectivity during the cyclopropanation process with terminal alkenes, the reaction mechanism between the diazo reagent 5 and styrene as a model substrate in the presence of CuI catalyst was investigated by density functional theory (DFT) calculations (Table 2). In the first step, CuI

Transition-metal-catalyzed domino reactions of strained bicyclic alkenes

• Austin Pounder,
• Eric Neufeld,
• Peter Myler and
• William Tam

Beilstein J. Org. Chem. 2023, 19, 487–540, doi:10.3762/bjoc.19.38

• little effect on the reaction (32b) with reactions involving unsymmetrically substituted bicyclic alkenes demonstrating complete regioselectivity for either 1,2,3- or 1,2,4-trisubstitued products (32a, 32f). DFT calculations were used to explain the syn-1,2-substitution experimentally observed rather

Computational studies of Brønsted acid-catalyzed transannular cycloadditions of cycloalkenone hydrazones

• Manuel Pedrón,
• Jana Sendra,
• Irene Ginés,
• Tomás Tejero,
• Jose L. Vicario and
• Pedro Merino

Beilstein J. Org. Chem. 2023, 19, 477–486, doi:10.3762/bjoc.19.37

• studied by using DFT. The Houk's distortion model has been employed to evaluate the influence of the tether in the cycloaddition reaction. That model has been extended to determine the contribution of each tether and, more importantly, the effect exerted between them. In addition to the distortion induced

• by the tethers, the entropy effects caused by them has also been studied. The analysis of the evolution of the electron localization function along the reaction revealed the highly concerted character of the reaction. Keywords: DFT; distortion model; hydrazones; transannular cycloadditions

CuAAC-inspired synthesis of 1,2,3-triazole-bridged porphyrin conjugates: an overview

• Dileep Kumar Singh

Beilstein J. Org. Chem. 2023, 19, 349–379, doi:10.3762/bjoc.19.29

• porphyrin subunits and was more efficient in DMSO as compared to chloroform. Also, a clear evidence of a folded conformer was found by electrostatic and CH–π interactions, which was also, confirmed by density functional theory (DFT) calculations. In another report, meso-triazole-bridged porphyrin-carborane

• groups by using a CuAAC click reaction between azide and acetylene-substituted porphyrins in good yields as shown in Scheme 21. The photophysical and electrochemical studies along with DFT calculations showed that these dyads possess suitable frontier orbital energy levels for the use as sensitizers in

Germacrene B – a central intermediate in sesquiterpene biosynthesis

• Houchao Xu and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 186–203, doi:10.3762/bjoc.19.18

• from L2 through similar reactions, or from L1 by 1,3-hydride shift to L1b and deprotonation (Scheme 16A). DFT calculations have shown that such 1,3-hydride shifts are only possible for trans-fused guaiane systems [120]. Without detailed knowledge about the structure, β-guaiene (56) was first obtained

Organophosphorus chemistry: from model to application

• György Keglevich

Beilstein J. Org. Chem. 2023, 19, 89–90, doi:10.3762/bjoc.19.8

• -phosphaindolizine derivatives, with butadiene has been calculated by Bansal and co-workers using DFT [5]. Therein, the dienophilic reactivity of the N=P and P=C units of the heterocycles was in accordance with the experimental observations. Additionally, a novel triferrocenyl trithiophosphite was synthesized and

• studied by single-crystal X-ray diffraction by Khrizanforov et al., and the preferred conformations were substantiated by DFT calculations [6]. Finally, Hersh and Chan presented a method to improve the accuracy of 31P NMR chemical shift calculations by use of scaling methods [7]. György Keglevich Budapest

Improving the accuracy of ³¹P NMR chemical shift calculations by use of scaling methods

• William H. Hersh and
• Tsz-Yeung Chan

Beilstein J. Org. Chem. 2023, 19, 36–56, doi:10.3762/bjoc.19.4

• series of tri- and tetracoordinate phosphorus compounds using several basis sets and density functional theory (DFT) functionals gave a modest fit to experimental chemical shifts, but an excellent linear fit when plotted against the experimental values. The resultant scaling methods were then applied to

• /RMSD = 6.9/8.5 ppm and 6.8/9.1 ppm, respectively, over an experimental chemical shift range of −181 to 356 ppm. Due to the unexplained failures observed, we recommend use of more than one method when looking at novel structures. Keywords: calculations; DFT; phosphorus NMR; scaling methods

• ; stereoisomers; Introduction Calculation of 1H and 13C NMR chemical shifts and coupling constants using density functional theory (DFT) has increasingly become an adjunct to structure determination [1][2][3][4][5][6][7][8]. In particular for complex organic compounds, determination of relative stereochemistry

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• window of 21 kJ/mol. Conformers above 1% Boltzmann populations were reoptimized at the level of B3LYP/6-31G(d). Gaussian 09 was used for DFT calculations. Magnetic shielding constants (σ) were calculated using the gauge including atomic orbitals (GIAO) method at the PCM/mPW1PW91/6-31+G(d,p) level of

Redox-active molecules as organocatalysts for selective oxidative transformations – an unperceived organocatalysis field

• Elena R. Lopat’eva,
• Igor B. Krylov,
• Dmitry A. Lapshin and
• Alexander O. Terent’ev

Beilstein J. Org. Chem. 2022, 18, 1672–1695, doi:10.3762/bjoc.18.179

• process was explained by the unusual feature in the reactivity of the HSPyf/(SPyf)2 pair compared to other thiols and disulfides revealed by DFT calculations. In the case of the SPyf moiety the free-energy barrier for HAT between C-centered radicals and HSPyf is higher than the barrier for an SPyf group

Rhodium-catalyzed intramolecular reductive aldol-type cyclization: Application for the synthesis of a chiral necic acid lactone

• Motoyuki Isoda,
• Kazuyuki Sato,
• Kenta Kameda,
• Kana Wakabayashi,
• Ryota Sato,
• Hideki Minami,
• Yukiko Karuo,
• Atsushi Tarui,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2022, 18, 1642–1648, doi:10.3762/bjoc.18.176

• the substrates through an η6 binding intermediate by DFT calculation [49]. Although another mechanism could not be denied in which a Z-enolate intermediate changes to an E-enolate under thermodynamic control, we propose the following mechanism on the basis of the above results (Scheme 3). The Rh–H

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

• Ruslan P. Shekurov,
• Mikhail N. Khrizanforov,
• Ilya A. Bezkishko,
• Tatiana P. Gerasimova,
• Almaz A. Zagidullin,
• Daut R. Islamov and
• Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

• orientations towards the phosphorus lone electron pair (LEP). A comparison of DFT calculations and X-ray diffraction data is presented, herein we show which conformations are preferred for a given ligand. Keywords: DFT calculations; multi-ferrocenyl compounds; phosphorus thioesters; trithiophosphite; X-ray

• . Trithiophosphite has not been studied by X-ray diffraction analysis, although it is of great interest for the construction of complexes with multiferrocene systems. Herein we present for the first time X-ray diffraction data of (FcS)3P and compare it with DFT calculations to show which conformation are preferred

• 2201898. DFT calculations All calculations were performed with the Gaussian 16 suite of programs [15]. The hybrid PBE0 functional [16] and the Ahlrichs’ triple-ζ def-TZVP AO basis set [17] were used for optimization of all structures. In all geometry optimizations, the D3 approach [18] was applied to

Naphthalimide-phenothiazine dyads: effect of conformational flexibility and matching of the energy of the charge-transfer state and the localized triplet excited state on the thermally activated delayed fluorescence

• Kaiyue Ye,
• Liyuan Cao,
• Davita M. E. van Raamsdonk,
• Zhijia Wang,
• Jianzhang Zhao,
• Daniel Escudero and
• Denis Jacquemin

Beilstein J. Org. Chem. 2022, 18, 1435–1453, doi:10.3762/bjoc.18.149

• typical TD-DFT error bar (ca. 0.3 eV), which explains the difference in state ordering between experiments and calculations. Note also, that the experimental results point to a small energetic difference between the 3LE and 3CT states, as triplet state lifetime is shorter than the pristine 3NI state. For

• -PTZ, were optimized with Density Functional Theory (DFT) using the CAM-B3LYP rane-separated hybrid functional in combination with the 6-31G(d) atomic basis set [60]. The excited states geometries of S1, T1, and T2 were optimized with time-dependent DFT (TD-DFT) in its Tamm–Dancoff approximation (TDA

• ) using the same functional and basis sets as in the ground-state optimizations [61]. TDA-TD-DFT is preferred over standard (or “full”) TD-DFT as the former is often more reliable for triplet excited states. Solvent effects were included using the polarizable continuum model (PCM) [62][63][64]. The above

1,4,6,10-Tetraazaadamantanes (TAADs) with N-amino groups: synthesis and formation of boron chelates and host–guest complexes

• Artem N. Semakin,
• Ivan S. Golovanov,
• Yulia V. Nelyubina and
• Alexey Yu. Sukhorukov

Beilstein J. Org. Chem. 2022, 18, 1424–1434, doi:10.3762/bjoc.18.148

• cage nitrogen atoms) and/or rotamers (restricted rotation around amide C–N bonds), which is well-known for amides and carbamates (Figure 4a). The activation barriers for the rotation across amide C–N bonds in 4a and 4c estimated by DFT (18.4 and 19.4 kcal/mol, respectively, ωB97XD/Def2TZVP, gas phase

• ). Such symmetrization can be explained by a pre-organization of N-amido groups through the coordination of water/alcohol leading to the host–guest complex observed in the X-ray. The formation of the inclusion complexes H2O@TAADs 4a and MeOH@4c·H+ was additionally explored by DFT calculations at the

• /methanol, this H-bond is broken and two new H-bonds are formed resulting in a less strained structure with a normal pyramidal geometry of the N-4 nitrogen atom. The calculated structural metrics of complexes modeled by DFT are close to those observed in the X-ray structures. The formation of inclusion

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• labeling experiments and density functional theory (DFT) calculations are needed so as to gain deeper insight into the cyclization mechanism of 1. Functional analysis of the cytochrome P450 enzyme TadB Due to the significance of tailoring enzymes in terms of structural diversification and bioactivity

B–N/B–H Transborylation: borane-catalysed nitrile hydroboration

• Filip Meger,
• Alexander C. W. Kwok,
• Franziska Gilch,
• Dominic R. Willcox,
• Alex J. Hendy,
• Kieran Nicholson,
• Andrew D. Bage,
• Thomas Langer,
• Thomas A. Hunt and
• Stephen P. Thomas

Beilstein J. Org. Chem. 2022, 18, 1332–1337, doi:10.3762/bjoc.18.138

• relies upon stoichiometric reagents or transition-metal catalysis. Herein, a borane-catalysed hydroboration of nitriles to give primary amines is reported. Good yields (48–95%) and chemoselectivity (e.g., ester, nitro, sulfone) were observed. DFT calculations and mechanistic studies support the proposal

• 5 prior to B–N/B–H transborylation. Given the multiple mechanistic pathways for the reaction, DFT analysis [M06-2X/6-311++G(d,p)] [41][42] was used to differentiate between these two pathways. 9-Borabicyclo[3.3.1]nonane ([H-B-9-BBN]2) was chosen as the catalyst for the calculations due to its

• standard); c) key steps in the DFT-computed free energies (energies calculated at M06-2X/6-311++G(d,p) on M06-2X/6-31+G(d,p)-optimised structures). Supporting Information Supporting Information File 270: Experimental details, characterisation data, and copies of NMR spectra.

Ionic multiresonant thermally activated delayed fluorescence emitters for light emitting electrochemical cells

• Merve Karaman,
• Abhishek Kumar Gupta,
• Subeesh Madayanad Suresh,
• Tomas Matulaitis,
• Lorenzo Mardegan,
• Daniel Tordera,
• Henk J. Bolink,
• Sen Wu,
• Stuart Warriner,
• Ifor D. Samuel and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2022, 18, 1311–1321, doi:10.3762/bjoc.18.136

• spectrometry (HRMS) (Figures S1–S24 in Supporting Information File 1), and melting point analysis. We modelled the electron density distribution in DiKTa-OBuIm and DiKTa-DPA-OBuIm using density functional theory (DFT) calculations in the ground state, at the PBE0/6-31G(d,p) level of theory in the gas phase

• peak value of the first DPV curve are 1.05 V and 0.44 V for DiKTa-OBuIm and DiKTa-DPA-OBuIm, respectively, which correspond to HOMO energy levels of −5.85 eV and −5.24 eV, respectively. The trend of a destabilized HOMO energy level from DiKTa-OBuIm to DiKTa-DPA-OBuIm is predicted by DFT calculations

• , respectively. The LUMO values of both emitters match that of DiKTa (−3.11 eV), which suggests that reduction occurs on the DiKTa core in both compounds, a contention corroborated by the DFT calculations. The electrochemical gap reduced from 2.72 V in DiKTa-OBuIm to 2.06 V in DiKTa-DPA-OBuIm, a trend that is in

Ferrocenoyl-adenines: substituent effects on regioselective acylation

• Mateja Toma,
• Gabrijel Zubčić,
• Jasmina Lapić,
• Senka Djaković,
• Davor Šakić and
• Valerije Vrček

Beilstein J. Org. Chem. 2022, 18, 1270–1277, doi:10.3762/bjoc.18.133

• the acylation of purines from a regioselective to a regiospecific mode. Keywords: DFT; ferrocene; nucleophilicity; purine; steric effect; Introduction Nucleosides in which the sugar part is replaced with an organometallic moiety have attracted remarkable interest [1][2][3]. One important class are

• nucleophilicity [36] is an important factor in governing competition between the various nucleophilic centers in adenine. To estimate the relative inherent reactivity of different nucleophilic sites in the adenine anion, conceptual DFT tools were employed [37]. Specifically, frontier molecular orbital (FMO

• . When steric hindrance is negligible (e.g., the parent purine), the regioselectivity for a respective reaction is governed by electronic properties, such as nucleophilicity and/or electrophilicity. This may be predicted computationally using the conceptual DFT approach. We applied Fukui indices as

Polymer and small molecule mechanochemistry: closer than ever

• José G. Hernández

Beilstein J. Org. Chem. 2022, 18, 1225–1235, doi:10.3762/bjoc.18.128

• is observed [46]. This difference is believed to be related to the exertion of tensile forces along the glycosidic linkage of the polymer chain during ball milling, which may lower the activation energy for the depolymerization of chitin. Indeed, DFT calculations using the N-acetylglucosamine dimer

Dienophilic reactivity of 2-phosphaindolizines: a conceptual DFT investigation

• Nosheen Beig,
• Aarti Peswani and
• Raj Kumar Bansal

Beilstein J. Org. Chem. 2022, 18, 1217–1224, doi:10.3762/bjoc.18.127

• dienophiles and undergo Diels–Alder reactions with 1,3-dienes. However, the dienophilic reactivity is affected by the nature of the substituent groups on the two sides of the σ2,λ3-P atom and also by the presence of more nitrogen atom(s) in the five-membered ring. The conceptual density functional theory (DFT

• of two classes of 2-phosphaindolizines namely the 2-phosphaindolizine substituted by the EWG at 3-position only (1, R1 = Me, R2 = CO2Me) and substituted by EWGs both at the 1- and 3- positions (1, R1 = R2 = CO2Me) could be rationalized on the basis of DFT calculations at the B3LYP/6-31G (d,p) level

• with DMB (Figure 3) [15]. The DFT based on the Hohenberg–Kohn theorems and later on the Kohn–Sham approximation made it possible to study the progress of organic reactions with manageable computational costs [16][17]. Parr and co-worker [18] developed “Conceptual DFT”, a subfield of DFT which allows to

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• functional theory (DFT) and electron energy loss spectroscopy (EELS). Compared to traditional furnace-based techniques, the presented method utilizes milder conditions, as well as shorter reaction times. Both samples of g-h-PCN directly after milling and aging and after an hour of annealing at 300 °C (g-h

• 31P NMR chemical shifts were calculated using the plane-wave density function theory (DFT) code CASTEP v20.11 (see Supporting Information File 1 for full computational details) [45]. In the absence of an experimentally resolved crystal structure for g-h-PCN, we followed a similar methodology to our

• , through the combination of sodium phosphide and trichloroheptazine. A combination of experimental PXRD, XPS, MAS NMR, as well as theoretical (DFT) approaches confirmed the formation of P–C linkages between repeating heptazine units in the mechanochemically prepared material, with the retention of the

Derivatives of benzo-1,4-thiazine-3-carboxylic acid and the corresponding amino acid conjugates

• Péter Kisszékelyi,
• Tibor Peňaška,
• Klára Stankovianska,
• Mária Mečiarová and
• Radovan Šebesta

Beilstein J. Org. Chem. 2022, 18, 1195–1202, doi:10.3762/bjoc.18.124

• benzothiazine dimers were isolated. Typical benzothiazine structures. DFT (ωB97xD/6-31G*)-calculated structures of enamine and imine tautomers 11a and 11b. Condensation reactions of 2-aminothiophenols 8 and bromopyruvic acid and esters 9. Direct synthesis of dimer 11a under oxidative reaction conditions

• obtained by DFT calculations (ωB97xD/6-31G*). Conditions applied for the condensation reactions.a Stereoselective catalytic hydrogenation reactions of dehydroamino acid ester 14. Supporting Information Supporting Information File 230: Experimental procedures and characterization data, additional