The DP5 Probability, Quantification and Visualisation of Structural Uncertainty in Single Molecules

Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra. The widely-used DP4 algorithm will choose the best match from a series of possibilities, but draws no conclusions from a single candidate structure. Here we present the DP5 probability, a step-change in the quantification of molecular uncertainty: given one structure and one 13C NMR spectra, DP5 gives the probability of the structure being correct. We show the DP5 probability can rapidly differentiate between structure proposals indistinguishable by NMR to an expert chemist. We also show in a number of challenging examples the DP5 probability may prevent incorrect structures being published and later reassigned. DP5 will prove extremely valuable in fields such as discovery-driven automated chemical synthesis and drug development. Alongside the DP4-AI package, DP5 can help guide synthetic chemists when resolving the most subtle structural uncertainty. The DP5 system is available at https://github.com/Goodman-lab/DP5.

The DP5 Probability, Quantification and Visualisation of Structural Uncertainty in Single Molecules

Whenever a new molecule is made, a chemist will justify the proposed structure by analysing the NMR spectra. The widely-used DP4 algorithm will choose the best match from a series of possibilities, but draws no conclusions from a single candidate structure. Here we present the DP5 probability, a step-change in the quantification of molecular uncertainty: given one structure and one 13C NMR spectra, DP5 gives the probability of the structure being correct. We show the DP5 probability can rapidly differentiate between structure proposals indistinguishable by NMR to an expert chemist. We also show in a number of challenging examples the DP5 probability may prevent incorrect structures being published and later reassigned. DP5 will prove extremely valuable in fields such as discovery-driven automated chemical synthesis and drug development. Alongside the DP4-AI package, DP5 can help guide synthetic chemists when resolving the most subtle structural uncertainty. The DP5 system is available at https://github.com/Goodman-lab/DP5.

Conformational Analysis of [60]PCBM from DFT Simulations of Electronic Energies, Bond Strain and the 13C NMR Spectrum: Input Geometry Determination and Ester Bond Rotation Dynamics

With the aim of determining the best input geometry for DFT calculations of [60]PCBM, the geometry of 24 chemically possible [60]PCBM conformers were optimised and their electronic energies and average bond strains were determined. A DFT analysis of the relevant dihedral angles provided insights into the dynamical behaviour of the ester group through sterically restricted bond rotations. In addition, the 13C NMR spectra of the six better performing conformers were simulated and compared with an experiment. There is a close correlation between average bond strain, total electronic energy and mean absolute error of the simulated 13C NMR spectra of the ester carbons. The best overall candidate conformer for the input geometry had the C61-C4, C4-C3 and C3-C2 single bonds of the alkyl chain in syn, anti and anti arrangements, respectively, and had the C2-C1 and C1-O single bonds of the ester in syn and anti arrangements, respectively. This contrasts strikingly with most representations of PCBM in the literature, which depict all relevant bonds in anti arrangements.

Synthesis, Structures, and Antibacterial Activities of Hydrazone Compounds Derived from 4-Dimethylaminobenzohydrazide

A series of three new hydrazone compounds derived from the condensation reactions of 4-dimethylaminobenzohydrazide with 4-dimethylaminobenzaldehyde, 2-chloro-5-nitrobenzaldehyde and 3-methoxybenzaldehyde, respectively, were prepared. The compounds were characterized by elemental analysis, infrared and UV-vis spectra, HRMS, 1H NMR and 13C NMR spectra, and single crystal X-ray diffraction. Crystals of the compounds are stabilized by hydrogen bonds. The compounds were assayed for antibacterial (Bacillus subtilis, Escherichia coli, Pseudomonas fluorescence and Staphylococcus aureus) and antifungal (Aspergillus niger and Candida albicans) activities by MTT method. The results indicated that compound 2 is an effective antibacterial material.

Synthesis of C2-Symmetrical Bis-(β-Enamino-Pyran-2,4-dione) Derivative Linked via 1,6-Hexylene Spacer: X-ray Crystal Structures, Hishfeld Studies and DFT Calculations of Mono- and Bis-(Pyran-2,4-diones) Derivatives

The synthesis of C2-symmetrical bis(β-enamino-pyran-2,4-dione) derivative 3 connected via 1,6-hexylene linker was reported for the first time. X-ray structures and Hirshfeld studies of the new bis- β-enamino-pyran-2,4-dione derivative 3 along with two structurally related pyran-2,4-dione derivatives 2a,b were discussed. A comparative analysis of the different intermolecular contacts affecting the crystal stability was presented. Generally, the H…H, O…H, and H…C interactions are common in all compounds and are considered the most abundant contacts. In addition, DFT calculations were used to compute the electronic properties as well as the 1H and 13C NMR spectra of the studied systems. All compounds (except 3) are polar where 2a (3.540 Debye) has a higher dipole moment than 2b (2.110 Debye). The NMR chemical shifts were calculated and excellent correlations between the calculated and experimental data were obtained (R2 = 0.93–0.94).

Synthesis of Novel N-Acylhydrazones and Their C-N/N-N Bond Conformational Characterization by NMR Spectroscopy

In this article, a synthesis of N’-(benzylidene)-2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazides and their structural interpretation by NMR experiments is described in an attempt to explain the duplication of some peaks in their 1H- and 13C-NMR spectra. Twenty new 6-methyl-1H-pyrazolo[3,4-b]quinoline substituted N-acylhydrazones 6(a–t) were synthesized from 2-chloro-6-methylquinoline-3-carbaldehyde (1) in four steps. 2-Chloro-6-methylquinoline-3-carbaldehyde (1) afforded 6-methyl-1H-pyrazolo[3,4-b]quinoline (2), which upon N-alkylation yielded 2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetate (3). The hydrazinolysis of 3 followed by the condensation of resulting 2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazide (4) with aromatic aldehydes gave N-acylhydrazones 6(a–t). Structures of the synthesized compounds were established by readily available techniques such as FT-IR, NMR and mass spectral studies. The stereochemical behavior of 6(a–t) was studied in dimethyl sulfoxide-d6 solvent by means of 1H NMR and 13C NMR techniques at room temperature. NMR spectra revealed the presence of N’-(benzylidene)-2-(6-methyl-1H-pyrazolo[3,4-b]quinolin-1-yl)acetohydrazides as a mixture of two conformers, i.e., E(C=N)(N-N) synperiplanar and E(C=N)(N-N)antiperiplanar at room temperature in DMSO-d6. The ratio of both conformers was also calculated and E(C=N) (N-N) syn-periplanar conformer was established to be in higher percentage in equilibrium with the E(C=N) (N-N)anti-periplanar form.

2-Hydroxy-3-octyloxybenzaldehyde

Herein, we report the chromatography-free synthesis of 2-hydroxy-3-octyloxybenzaldehyde by the alkylation of 2,3-dihydroxybenzaldehyde as a promising precursor for new SalEn-type complexes with transition metals. The structure of the product is elucidated by means of 1H and 13C-NMR spectra, high-resolution mass spectrometry with electrospray ionization (ESI-HRMS) and Fourier-transform infrared spectroscopy (FTIR).