Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

• Michał M. Więcław and
• Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

• of the product as a chair (1C4, 4C1) or a skew-boat (1S3, 3S1) conformer, of which the former is favored, as it proceeds via the lower-energetic chair-like transition state. The favored path of action will result in addition syn or anti to the substituent in position 5, depending on the starting

• spontaneous decomposition of the zirconium complex INT-1-A to the free imine species INT-3. This process is much more likely to occur via the 5-membered cyclic transition state TS-1-A than the alternative TS-1-B, as the energy barrier of 60.1 kcal·mol−1 is definitely too high for the reaction to take place

Deoxyfluorination of acyl fluorides to trifluoromethyl compounds by FLUOLEAD^®/Olah’s reagent under solvent-free conditions

• Yumeng Liang,
• Akihito Taya,
• Zhengyu Zhao,
• Norimichi Saito and
• Norio Shibata

Beilstein J. Org. Chem. 2020, 16, 3052–3058, doi:10.3762/bjoc.16.254

• an intermediate III via transition state II. The intermediate III is further activated by (HF)n to form IV, which finally induces the deoxyfluorination via V furnishing the trifluoromethylated products 2 with the release of ArS(O)F and (HF)n. Conclusion We have reported an efficient protocol for the

Recent developments in enantioselective photocatalysis

• Callum Prentice,
• James Morrisson,
• Andrew D. Smith and
• Eli Zysman-Colman

Beilstein J. Org. Chem. 2020, 16, 2363–2441, doi:10.3762/bjoc.16.197

• al. [94] it is suggested that this reaction uses 1O2 for the oxidation, and proceeds through transition state 219‡ for the hydrogen-bonded catalysed nucleophilic addition step. Jiang et al. recently applied a similar dual catalytic system to the dehalogenative protonation of α,α-chlorofluoro ketones

• •−, which adds to the nitrone via a proposed 6-membered transition state to afford radical cation 286•+. Subsequent hydrogen atom abstraction from TEEDA•+ generates complex 286−. Protonation and displacement by other substrate molecules releases the desired 1,2-amino alcohol products 287 in excellent yields

Photosensitized direct C–H fluorination and trifluoromethylation in organic synthesis

• Shahboz Yakubov and
• Joshua P. Barham

Beilstein J. Org. Chem. 2020, 16, 2151–2192, doi:10.3762/bjoc.16.183

• parameters of para substituents [197], and therefore the reaction success could relate to the transition state of the benzylic radical’s fluorination step. Given later studies [147][198][199], it cannot be ruled out that this reaction could be interpreted as a photosensitized C–H fluorination involving the

• fluorination [46][205]. The selectivity for β- or γ-fluorination could be attributed to an interaction of the breaking C(sp3)–H bond and the neighboring ketone, which is part of the proposed 5- and 6-membered transition state, respectively. When the 5- and the 6-membered transition state is possible, the free

• . The authors demonstrated that the transition state for Selectfluor® undergoing HAT at this position (see TS1) was more kinetically accessible, despite the bond dissociate free energies (BDFEs) suggesting C3 functionalization (Scheme 27). 3.4 Directing-group-guided benzylic C–H fluorination In another

Reactions of 3-aryl-1-(trifluoromethyl)prop-2-yn-1-iminium salts with 1,3-dienes and styrenes

• Thomas Schneider,
• Michael Keim,
• Bianca Seitz and
• Gerhard Maas

Beilstein J. Org. Chem. 2020, 16, 2064–2072, doi:10.3762/bjoc.16.173

• of 1a and 2,3-dimethylbutadiene (DMBD), the regioselectivity of which is as expected for a highly asynchronous transition state with effective stabilization of the positive charge or a two-step ionic process (vide infra). The high electrophilic power of the 1-CF3-substituted propyn-1-iminium ion

Natural dolomitic limestone-catalyzed synthesis of benzimidazoles, dihydropyrimidinones, and highly substituted pyridines under ultrasound irradiation

• Kumar Godugu,
• Venkata Divya Sri Yadala,
• Mohammad Khaja Mohinuddin Pinjari,
• Trivikram Reddy Gundala,
• Lakshmi Reddy Sanapareddy and
• Chinna Gangi Reddy Nallagondu

Beilstein J. Org. Chem. 2020, 16, 1881–1900, doi:10.3762/bjoc.16.156

• confirmed that the reaction stopped at the bisimine I stage. This was due to the intramolecular hydrogen bonding between the hydrogen atom of the ortho-hydroxy group and the nitrogen atom of the imine group in a six-membered ring transition state [87]. Similarly, the reaction between 3-ethoxysalicylaldehyde

Stereoselective Biginelli-like reaction catalyzed by a chiral phosphoric acid bearing two hydroxy groups

• Xiaoyun Hu,
• Jianxin Guo,
• Cui Wang,
• Rui Zhang and
• Victor Borovkov

Beilstein J. Org. Chem. 2020, 16, 1875–1880, doi:10.3762/bjoc.16.155

• yield and enantioselectivity of the reaction dropped dramatically, hence confirming our initial proposal that the free hydroxy groups in the chiral phosphoric acid 3 played an important role in this enantioselective transformation. Based on these results, a plausible transition-state structure was

• ) H bondings with the enolizable ketone, respectively. This rigid chiral transition-state structure favored the stereoselective attack of the enol on the imine. Once the two hydroxy groups were etherified, the loss of the rigid structure would lead to low enantioselectivity. Additionally, this

• solvent, the residue was purified by column chromatography using petroleum ether/ethyl acetate 6:1–3:1. A plausible chiral transition-state structure in the Biginelli-like reaction catalyzed by phosphoric acid 3. Synthesis of chiral phosphoric acid 3. Synthesis of methylated chiral phosphoric acid 7

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• substrate of mycobacterial galactofuranosyltransferase GlfT2 in the transition state, we evaluated these compounds by computational methods, as well as in an enzyme assay for the possible inhibition of the mycobacterial galactan biosynthesis. Our data show that despite favorable docking scores to the active

• site of GlfT2, none of these compounds serve as efficient inhibitors of the enzymes involved in the mycobacterial galactan biosynthesis. Keywords: GlfT2; molecular modeling; mycobacterium tuberculosis; synthesis; transition state inhibitors; Introduction Tuberculosis (TB) is one of the most prevalent

• mechanism studies using computational chemistry methods. The probable reaction mechanisms were studied by hybrid DFT QM/MM molecular dynamics simulations [11] where the possible transition state (TS) structures were localized. The observation of the possible TS structure opens the opportunities for the in

Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines

• Vladimir Kubyshkin

Beilstein J. Org. Chem. 2020, 16, 1837–1852, doi:10.3762/bjoc.16.151

• trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pKa values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors

• water). At the same time, the amide rotation is a simple process with only one (prevalent) transition state and two ground states [93]. The high level of the energetic barrier implies that there is only a negligible subpopulation of molecules that may be involved in the transition, and therefore the

• rotation velocity. The difference was especially prominent in the trifluoromethylated species, 3 and 4 (see Table 3). Curiously, it is not possible to explain this finding by considering the ground state, thus the so-called syn/exo transition state [96] should be analyzed instead. The data make sense, if

One-pot synthesis of oxazolidinones and five-membered cyclic carbonates from epoxides and chlorosulfonyl isocyanate: theoretical evidence for an asynchronous concerted pathway

• Esra Demir,
• Ozlem Sari,
• Yasin Çetinkaya,
• Ufuk Atmaca,
• Safiye Sağ Erdem and
• Murat Çelik

Beilstein J. Org. Chem. 2020, 16, 1805–1819, doi:10.3762/bjoc.16.148

• onto C1 or C2 and an attack of O3 on C5 occur in an asynchronous concerted manner. The first transition state (TS1) corresponds to the nucleophilic attack of N4 onto the C2 of 7f leading to oxazolidinone intermediate 10. The alternative transition state (TS1′) corresponds to the nucleophilic attack of

• the transition state and so lowering the activation energy barrier (Figure 3a). On the other hand, stabilization of the benzylic cation is not possible along the IRC path for TS1′ (Figure 3b), since the bond distance C2–C(Ph) is found as around 1.50 Å showing a single bond character. This can be the

• main reason for the predominant formation of intermediate 10 which results in the regioselective formation of oxazolidinone 9f Optimized geometries for reactant complex RC1 (7f+CSI), transition state TS1 and 10 for the selected path are depicted in Figure 4. This step is common for all paths studied

Pauson–Khand reaction of fluorinated compounds

• Jorge Escorihuela,
• Daniel M. Sedgwick,
• Alberto Llobat,
• Mercedes Medio-Simón,
• Pablo Barrio and
• Santos Fustero

Beilstein J. Org. Chem. 2020, 16, 1662–1682, doi:10.3762/bjoc.16.138

• repulsions that occur in the equatorial position. Consequently, in the most favorable transition state there is no steric hindrance between the CF3 group and the ethylenic hydrogen, leading to the observed diastereoisomer. On the other hand, the use of 1,9-enyne 18c (n = 3) did not afford the corresponding

Fluorohydration of alkynes via I(I)/I(III) catalysis

• Jessica Neufeld,
• Constantin G. Daniliuc and
• Ryan Gilmour

Beilstein J. Org. Chem. 2020, 16, 1627–1635, doi:10.3762/bjoc.16.135

• and 9, respectively, Figure 3A). Deletion of the ester carbonyl (10) and replacement of the phenyl group by methyl (11) was also detrimental. From these data it is tempting to speculate upon the involvement of a chair-like transition state in which the intramolecular interaction of the phenyl π-system

In silico rationalisation of selectivity and reactivity in Pd-catalysed C–H activation reactions

• Liwei Cao,
• Mikhail Kabeshov,
• Steven V. Ley and
• Alexei A. Lapkin

Beilstein J. Org. Chem. 2020, 16, 1465–1475, doi:10.3762/bjoc.16.122

• a relatively unstable intermediate (Figure 1) [26], the Hammond postulate can be applied to the electrophilic substitution reactions. The Hammond postulate states that a transition state will be structurally and energetically similar to the species (reactant, intermediate or product) nearest to it

Highly selective Diels–Alder and Heck arylation reactions in a divergent synthesis of isoindolo- and pyrrolo-fused polycyclic indoles from 2-formylpyrrole

• Carlos H. Escalante,
• Eder I. Martínez-Mora,
• Carlos Espinoza-Hicks,
• Alejandro A. Camacho-Dávila,
• Fernando R. Ramos-Morales,
• Francisco Delgado and
• Joaquín Tamariz

Beilstein J. Org. Chem. 2020, 16, 1320–1334, doi:10.3762/bjoc.16.113

• . Accordingly, the R2 substituent in the diene would play an important role in directing the endo/exo orientation of the approach to the maleimide at the transition state (TS). Therefore, the endo diastereoselectivity is apparently not controlled by the presence or the absence of the substituent bonded to the

Fluorinated phenylalanines: synthesis and pharmaceutical applications

• Laila F. Awad and
• Mohammed Salah Ayoup

Beilstein J. Org. Chem. 2020, 16, 1022–1050, doi:10.3762/bjoc.16.91

• -protected acid 120 in good yield. Finally, removal of the Boc group then generated the free amino acid (3R)-3-fluoro-ʟ-phenylalanine (121) [64] (Scheme 27). Okuda’s group used 121 in the synthesis of a nucleoside that could be used to assess the transition state of a ribosome-catalyzed peptide-bond

Aldehydes as powerful initiators for photochemical transformations

• Maria A. Theodoropoulou,
• Nikolaos F. Nikitas and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2020, 16, 833–857, doi:10.3762/bjoc.16.76

• compound 44 and a triplet state olefin molecule 17 in a nonplanar configuration. Both processes, oxetane formation and isomerization, were thought to proceed via the triplet state of benzaldehyde. The alternative pathway includes a polarization of the π-system of the olefin, forming a transition state

Preparation of 2-phospholene oxides by the isomerization of 3-phospholene oxides

• Péter Bagi,
• Réka Herbay,
• Nikolett Péczka,
• Zoltán Mucsi,
• István Timári and
• György Keglevich

Beilstein J. Org. Chem. 2020, 16, 818–832, doi:10.3762/bjoc.16.75

• rearrangement, involving zwitterionic structure 11 via high energy and a four-membered ring transition state [TS(1→11)]. This stressed structure has a rigid, entropically unbeneficial transition. The second transition state [TS(11→4)] represents a significantly lower energy gap with a more comfortable five

• atom can be easily protonated via a high enthalpy transition state [TS(17→18)], which is the rate determining step of this reaction sequence. We suppose that this rather high enthalpy is much lower due to the tunneling effect of the proton, whose energy gap is estimated to be reduced to about 130 kJ

• mol−1 in an optimal arrangement of the proton [73][74]. After the transition state, the mesylate anion attacks consecutively the position C(3), forming a neutral, relatively low-enthalpy intermediate 18. The departure of the mesylate anion from position C(3) attracts the proton from C(2) via a lower

Recent advances in Cu-catalyzed C(sp³)–Si and C(sp³)–B bond formation

• Balaram S. Takale,
• Ruchita R. Thakore,
• Elham Etemadi-Davan and
• Bruce H. Lipshutz

Beilstein J. Org. Chem. 2020, 16, 691–737, doi:10.3762/bjoc.16.67

• from the directing group. This was attributed to the importance of both the negative charge at the carbon and the forming C–Cu bond being developed in the transition state, which is stabilized by the positive charge on the carbon bearing the directing group. Later, in 2017, the same group investigated

• addition of benzylic–Cu intermediates to imines proceeds through a flexible linear transition state which is sensitive to the steric environment surrounding the copper catalyst. This observation provided the opportunity to achieve either diastereomer depending on the choice of the ligand L45 or L46. Based

Copper-catalyzed remote C–H arylation of polycyclic aromatic hydrocarbons (PAHs)

• Anping Luo,
• Min Zhang,
• Zhangyi Fu,
• Jingbo Lan,
• Di Wu and
• Jingsong You

Beilstein J. Org. Chem. 2020, 16, 530–536, doi:10.3762/bjoc.16.49

• the carbonyl oxygen to I gives intermediate II, which undergoes an aryl-transfer reaction via a Heck-like four-membered-ring transition state III to form the intermediate IV with Cu(III) and aryl group added at the C8- and C7-positions of the naphthalene ring, respectively. Finally, the breakdown of

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• . From there, dissociation of the N–O bond starts to take place and proceeds uphill through a transition state, T1(TS), the structure of which was optimized fully. Vibrational analysis gives a single imaginary frequency (−550.12 cm−1) which corresponds to the N–O bond stretching confirming that the

• (TS) is reflected in the low value of the activation entropy, ΔS≠ = 0.474 cal/mol∙K, which means that there is a very small disorganization in the transition state as compared to the reactant in the T1 minimum state. The length of the bond N–O in the transition state is equal to 1.629 Å. The

• the bond under dissociation, that is, the N−O bond which constitutes the potential well. In Equation 4 Q≠ and QR represent the molecular partition functions in the transition state and in T1 min with their values being 0.241907∙1024 and 0.184606∙1024, respectively. Additionally, Equation 5 was used to

Efficient method for propargylation of aldehydes promoted by allenylboron compounds under microwave irradiation

• Jucleiton J. R. Freitas,
• Queila P. S. B. Freitas,
• Silvia R. C. P. Andrade,
• Juliano C. R. Freitas,
• Roberta A. Oliveira and
• Paulo H. Menezes

Beilstein J. Org. Chem. 2020, 16, 168–174, doi:10.3762/bjoc.16.19

• organometallics in solution resulting in mixtures of the two reagents [15]. Thus, upon reaction with an aldehyde, mixtures of propargylic and allenic alcohols can be obtained through a chelate transition state (SE2'). Attempts to improve the regioselectivity of the propargylation reaction by using allenic

The reaction of arylmethyl isocyanides and arylmethylamines with xanthate esters: a facile and unexpected synthesis of carbamothioates

• Narasimhamurthy Rajeev,
• Toreshettahally R. Swaroop,
• Ahmad I. Alrawashdeh,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Seegehalli M. Anil,
• Kuppalli R. Kiran,
• Chandra,
• Paris E. Georghiou,
• Kanchugarakoppal S. Rangappa and
• Maralinganadoddi P. Sadashiva

Beilstein J. Org. Chem. 2020, 16, 159–167, doi:10.3762/bjoc.16.18

• with Gaussian 09 [36]. The HF/6-31G(d) level of theory in the gas phase was only used to locate the transition state geometries. An intrinsic reaction coordinate (IRC) analysis was conducted for each transition state studied in this work to confirm that the transition states were associated with the

• model (PCM). Vibrational frequencies for all of the optimized structures were calculated to ensure the presence of a single imaginary frequency for each transition state, and the absence of imaginary frequencies for reactants, intermediates, and products and also to obtain thermal corrections for

• anion Int1 by hydride addition to the terminal carbon atom of the isocyanide group in 2a via transition state TS1. This anion undergoes nucleophilic addition to the thiocarbonyl moiety of the xanthate 1a to generate the intermediate Int2 via transition state TS2. In the next step, elimination of the

[1,3]/[1,4]-Sulfur atom migration in β-hydroxyalkylphosphine sulfides

• Katarzyna Włodarczyk,
• Piotr Borowski and
• Marek Stankevič

Beilstein J. Org. Chem. 2020, 16, 88–105, doi:10.3762/bjoc.16.11

• , according to calculations. The reason of this behavior was most probably the cyclic structure of the intermediate. However, if the intermediate I can undergo a second protonation process, intermediate III forms through transition state II. Water elimination from III proceeded with slight increase in energy

• , affording intermediate IV, which may undergo two different transformations: The first transformation involves dissociation of a water molecule, which leads to the formation of the dication IX through transition state VIII. Taking into account that all energy barriers were well below 10 kcal/mol, it seemed

• formed dication V underwent an intramolecular nucleophilic substitution through transition state VI, which proceeded with a small activation barrier, leading to the cyclic intermediate VII and further to the rearranged product 54. The tentative mechanism discussed above does not explain the formation of

Understanding the role of active site residues in CotB2 catalysis using a cluster model

• Keren Raz,
• Ronja Driller,
• Thomas Brück,
• Bernhard Loll and
• Dan T. Major

Beilstein J. Org. Chem. 2020, 16, 50–59, doi:10.3762/bjoc.16.7

• active site cluster model. The results revealed the significant effect of the active site residues on the relative electronic energy of the intermediates and transition state structures with respect to gas phase data. A detailed understanding of the role of the enzyme environment on the CotB2 reaction

• potential. Additionally, structural analysis revealed that each cation was stabilized by noncovalent interactions, such as π–cation and dipole–cation interactions. A comparison of the transition state structures in the gas phase vs the active site model is shown in Table 2. These findings suggest that the

• residues. Comparison table of transition state structures in gas phase vs active site model. Supporting Information Supporting Information File 180: Cartesian coordinates for all species. Funding This work was supported by the Israeli Science Foundation (Grant no. 1683/18).

Synthesis of C-glycosyl phosphonate derivatives of 4-amino-4-deoxy-α-ʟ-arabinose

• Lukáš Kerner and
• Paul Kosma

Beilstein J. Org. Chem. 2020, 16, 9–14, doi:10.3762/bjoc.16.2

• derivatives. These intermediates will be of value for their future conversion into transition state analogues as well as for the introduction of various lipid extensions at the anomeric phosphonate moiety. Keywords: antibiotic resistance; glycosyl phosphonate; glycosyl transferase; lipid A

• compounds to allow for future incorporation of different lipid chains and options towards glycal analogues as potential transition state analogues to inhibit 4-amino-4-deoxy-ʟ-arabinose transfer to bacterial LPS. Results and Discussion The previously synthesized [14] methyl 4-azido-4-deoxy-α-ʟ

• signal of the anomeric OH group at 5.79 ppm. Next, the ensuing elimination step was carried out to explore the access to transition state analogues [22] potentially mimicking the sp2 character of the oxocarbenium intermediate in the enzymatic transfer reaction. In addition, exo-glycals are versatile