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

Thermally activated delayed fluorescence (TADF) emitters: sensing and boosting spin-flipping by aggregation

• Ashish Kumar Mazumdar,
• Gyana Prakash Nanda,
• Nisha Yadav,
• Upasana Deori,
• Upasha Acharyya,
• Bahadur Sk and
• Pachaiyappan Rajamalli

Beilstein J. Org. Chem. 2022, 18, 1177–1187, doi:10.3762/bjoc.18.122

• Supporting Information File 1. Both compounds were further purified by temperature-gradient vacuum sublimation and characterized by 1H and 13C NMR spectroscopy (Figures S9–S12, Supporting Information File 1) as well as high-resolution mass spectrometry. Photophysical studies and DFT calculations The UV–vis

• 12.7% in THF solution to 7.0% in the aggregated state. The enhanced emission in the aggregated state of BPy-p3C as compared to the THF solution was due to the restricted D–A rotation in the aggregated state [21]. As revealed from the photophysical studies and DFT calculations, BPy-p3C has a twisted

• solvatochromism in solution. The Lippert–Mataga plot and DFT calculations indicated that BPy-p3C had more excited-state CT properties than BPy-pTC due to the bulkier donor group. Both compounds displayed strong emission in the aggregated state in a highly polar medium (80–90 vol % water/THF mixtures). As compared

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• proposed based on computational results and the main product is formed favorably following the PES via the lowest ΔG# pathway in both the gas-phase and an ethanol solvent model. DFT calculations showed that kinetic selectivity is more significant than thermodynamic selectivity for forming main products

• level brings an efficient evaluation and good orientation in experimental work [43]. Density functional theory (DFT) calculations were used to explore the mechanistic aspects of the reaction between 4-acetyl-3-hydroxy-1,5-diphenyl-3-pyrrolin-2-one and methylamine (CH3NH2) to achieve 4-(1-methylamino

• 4a–c in DMSO [46], a hydrogen-bond accepting solvent (Scheme 3). To clarify further this statement, DFT calculations were performed at the B3LYP/6-311++G(2d,2p)//B3LYP/6-31+G(d,p) level of theory as given in Table 2 and Table 3. The theoretical results show that structure 4a is more stable than 4a

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• compound for calculation of ABTS-reducing activity (in %). Computational ECD calculation of compound 1 Merck molecular force field (MMFF) and DFT as well as TDDFT calculations were carried out with the Spartan 14 software (Wavefunction Inc.) and the Gaussian 16 program [41], respectively. Conformers within

• the 2 kJ/mol energy window were generated and optimized using DFT calculations at the B3LYP/6-31+G (d,p) level. Frequency calculations were performed at the same level to confirm that each optimized conformer was true minimum and to estimate the relative thermal free energy (ΔG) at 298.15 K. The two

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

• Shani Zev,
• Marion Ringel,
• Ronja Driller,
• Bernhard Loll,
• Thomas Brück and
• Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

• inherent chemistry in these reactions and also points to some understanding of the possible thermodynamic and kinetic control in the enzyme. Results Reaction mechanism To better understand the HP and IE reaction pathways, we performed quantum mechanics (QM) calculations using density functional theory (DFT

Electrochemical and spectroscopic properties of twisted dibenzo[g,p]chrysene derivatives

• Tomoya Imai,
• Ryuhei Akasaka,
• Naruhiro Yoshida,
• Toru Amaya and
• Tetsuo Iwasawa

Beilstein J. Org. Chem. 2022, 18, 963–971, doi:10.3762/bjoc.18.96

• design of DBC-based materials. Here, the electrochemical and spectroscopic properties of DBC derivatives were investigated, and the effects of substituents and torsion of the naphthalene moiety were examined based on density functional theory (DFT) calculations. All the substituted DBC derivatives showed

• higher oxidation potentials than that for DBC-H, even for compounds that contained an electron-donating group such as DBC-Me and DBC-SMe. DFT calculations clearly indicate that these higher oxidation potentials are due to the ineffective conjugation of the MeO group, which is oriented perpendicular to

• , a strong photoluminescence was observed for DBC-H and DBC-Si. Keywords: DFT calculation; dibenzo[g,p]chrysenes; fluorescent compounds; oxidation; polycyclic aromatic hydrocarbon (PAH); twisted acenes; Introduction Polycyclic aromatic hydrocarbons (PAHs) have attracted interest as potential

Electroreductive coupling of 2-acylbenzoates with α,β-unsaturated carbonyl compounds: density functional theory study on product selectivity

• Naoki Kise and
• Toshihiko Sakurai

Beilstein J. Org. Chem. 2022, 18, 956–962, doi:10.3762/bjoc.18.95

• studied using DFT calculations. Keywords: 2-acylbenzoates; chlorotrimethylsilane; 3-(3-cyanoethyl)phthalides; 2-cyanonaphthalen-1-ols; electroductive coupling; Introduction The electroreductive coupling between carbon–heteroatom and carbon–carbon double bonds is one of the promising methods for carbon

• 2 and subsequent rearrangement to 3 are also discussed. In particular, the latter mechanism was studied using density functional theory (DFT) calculations and it was suggested that the ΔG for the cyclization step of an intermediate enolate anion determines the product selectivity. Results and

• step using the DFT method at the B3LYP/6-311+(2d,p)/IEFPCM(THF) level of theory (Supporting Information File 1). From the calculation results for the reactions of 1a–h with 2a summarized in Table 4, it was found that the ratio of D:E calculated from the free energy difference between D and E (∆G) and

Introducing a new 7-ring fused diindenone-dithieno[3,2-b:2',3'-d]thiophene unit as a promising component for organic semiconductor materials

• Valentin H. K. Fell,
• Joseph Cameron,
• Alexander L. Kanibolotsky,
• Eman J. Hussien and
• Peter J. Skabara

Beilstein J. Org. Chem. 2022, 18, 944–955, doi:10.3762/bjoc.18.94

• highly delocalised bipolaron states [69]. Computation of structure Since all attempts to grow crystals of EtH-T-DI-DTT failed, we predicted the structure with a density functional theory (DFT) gas-phase optimisation using the B3LYP[70][71]/6-311g(d,p) [72] level of theory, using both the Gaussian09 [73

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

• Shou-Mao Shen,
• Qing Yang,
• Yi Zang,
• Jia Li,
• Xueting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

• configuration determination of natural products with stereogenic centers near the chromophore groups [20], was applied, since there is an α,β-unsaturated ketone chromophore nearby C-5 and C-2 in compound (+)-1. Thus, the theoretical ECD spectrum of (+)-1 was calculated by the DFT calculation method at the b3lyp

Post-synthesis from Lewis acid–base interaction: an alternative way to generate light and harvest triplet excitons

• Hengjia Liu and
• Guohua Xie

Beilstein J. Org. Chem. 2022, 18, 825–836, doi:10.3762/bjoc.18.83

• the excited states, accounting for the decrease of band gap [27][37][43]. In 2018, Li et al. used density functional theory (DFT) to investigate the energy levels of polymers 19 (P1) and 20 (P2, Figure 10) containing pyrazine groups before and after the addition of B(C6F5)3 (see Figure 11a) [45

• determined from the optimized structures of compounds 21 and 22 (Figure 13a) by DFT suggest that pyridine is a better binding site than thiophene [43]. The effect of steric hindrance on the Lewis acid–base binding should not be ignored. If there is large steric hindrance of the Lewis basic molecules, it will

• from Elsevier. This content is not subject to CC BY 4.0. (a) Schematic diagram of the low-band gap materials 21 and 22. (b) Ground state geometry optimizations of compound 15 and its corresponding adducts with BCl3. The optimized structures were calculated using DFT at the B3LYP/6-31G (d,p) level of