scholarly journals NMR-TS: De Novo Molecule Identification from NMR Spectra

2020 ◽  
Author(s):  
Jinzhe Zhang ◽  
Kei Terayama ◽  
Masato Sumita ◽  
Kazuki Yoshizoe ◽  
Kengo Ito ◽  
...  
Keyword(s):  
Density Functional ◽  
Nmr Spectra ◽  
De Novo ◽  
Expert Knowledge ◽  
Chemical Space ◽  
Automated Identification ◽  
Functional Theory ◽  
Nmr Spectrum ◽  
Chemical Structures ◽  
Target Spectrum

<div>NMR spectroscopy is an effective tool for identifying molecules in a sample. Although many previously observed NMR spectra are accumulated in public databases, they cover only a tiny fraction of the chemical space, and molecule identification is typically accomplished manually based on expert knowledge. Herein, we propose NMR-TS, a machine-learning-based python library, to automatically identify any molecule from its NMR spectrum. NMR-TS discovers candidate molecules whose NMR spectra match the target spectrum by using deep learning and density functional theory (DFT)-computed spectra. As a proof-of-concept, we identify prototypical metabolites from their computed spectra. After an average 5451 DFT runs for each spectrum, six of the nine molecules are identified correctly, and proximal molecules are obtained in the other cases. This encouraging result implies that de novo molecule generation can contribute to the fully automated identification of chemical structures. NMR-TS is available at https://github.com/tsudalab/NMR-TS. <br></div>

scholarly journals NMR-TS: De Novo Molecule Identification from NMR Spectra

2020 ◽  
Author(s):  
Jinzhe Zhang ◽  
Kei Terayama ◽  
Masato Sumita ◽  
Kazuki Yoshizoe ◽  
Kengo Ito ◽  
...  
Keyword(s):  
Density Functional ◽  
Nmr Spectra ◽  
De Novo ◽  
Expert Knowledge ◽  
Chemical Space ◽  
Automated Identification ◽  
Functional Theory ◽  
Nmr Spectrum ◽  
Chemical Structures ◽  
Target Spectrum

<div>NMR spectroscopy is an effective tool for identifying molecules in a sample. Although many previously observed NMR spectra are accumulated in public databases, they cover only a tiny fraction of the chemical space, and molecule identification is typically accomplished manually based on expert knowledge. Herein, we propose NMR-TS, a machine-learning-based python library, to automatically identify any molecule from its NMR spectrum. NMR-TS discovers candidate molecules whose NMR spectra match the target spectrum by using deep learning and density functional theory (DFT)-computed spectra. As a proof-of-concept, we identify prototypical metabolites from their computed spectra. After an average 5451 DFT runs for each spectrum, six of the nine molecules are identified correctly, and proximal molecules are obtained in the other cases. This encouraging result implies that de novo molecule generation can contribute to the fully automated identification of chemical structures. NMR-TS is available at https://github.com/tsudalab/NMR-TS. <br></div>

scholarly journals 1,3,4-Thiadiazole-Containing Azo Dyes: Synthesis, Spectroscopic Properties and Molecular Structure

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2822
Author(s):  
Agnieszka Kudelko ◽  
Monika Olesiejuk ◽  
Marcin Luczynski ◽  
Marcin Swiatkowski ◽  
Tomasz Sieranski ◽  
...  
Keyword(s):  
Azo Dyes ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Spectroscopic Properties ◽  
Radiation Absorption ◽  
Functional Theory ◽  
Chemical Structures ◽  
Vis Spectroscopy ◽  
High Yields

Three series of azo dyes derived from 2-amino-5-aryl-1,3,4-thiadiazoles and aniline, N,N-dimethylaniline and phenol were synthesized in high yields by a conventional diazotization-coupling sequence. The chemical structures of the prepared compounds were confirmed by 1H-NMR, 13C-NMR, IR, UV-Vis spectroscopy, mass spectrometry and elemental analysis. In addition, the X-ray single crystal structure of a representative azo dye was presented. For explicit determination of the influence of a substituent on radiation absorption in UV-Vis range, time-dependent density functional theory calculations were performed.

scholarly journals UV–Vis Absorption Properties of New Aromatic Imines and Their Compositions with Poly({4,8-bis[(2-Ethylhexyl)oxy]Benzo[1,2-b:4,5-b′]Dithiophene-2,6-diyl}{3-Fluoro-2-[(2-Ethylhexyl)Carbonyl]Thieno[3,4-b]Thiophenediyl})

Materials ◽  
2019 ◽  
Vol 12 (24) ◽  
pp. 4191 ◽  
Author(s):  
Agnieszka Gonciarz ◽  
Robert Pich ◽  
Krzysztof Artur Bogdanowicz ◽  
Beata Jewloszewicz ◽  
Wojciech Przybył ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Organic Solar Cells ◽  
Density Functional ◽  
Bulk Heterojunction ◽  
Theoretical Calculations ◽  
Dft Methods ◽  
Functional Theory ◽  
Chemical Structures ◽  
Vis Spectroscopy ◽  
Aromatic Imines

In this paper, four new aromatic imines containing at least one thiazole-based heterocycle were analyzed in detail by UV–Vis spectroscopy, taking into consideration their chemical structures and interactions with PTB7, a known polymeric electron donor widely used in bulk heterojunction organic solar cells. It is demonstrated that the absorption spectra of the investigated active compositions can be modified not only by changing the chemical structure of imine, but also via formulations with PTB7. For all investigated imines and PTB7:imine compositions, calibration curves were obtained in order to find the optimum concentration in the composition with PTB7 for expansion and optimization of absorption spectra. All imines and PTB7:imine compositions were investigated in 1,2-dichlorobenzene by UV–Vis spectroscopy in various concentrations, monitoring the changes in the π–π* and n–π* transitions. With increasing imine concentrations, we did not observe changes in absorption maxima, while with increasing imine concentrations, a hypochromic effect was observed. Finally, we could conclude that all investigated compositions exhibited wide absorptions of up to 800 nm and isosbestic points in the range of 440–540 nm, confirming changes in the macromolecular organization of the tested compounds. The theoretical calculations of their vibration spectra (FTIR) and LUMO–HOMO levels by Density Functional Theory (DFT) methods are also provided. Finally, IR thermal images were measured for organic devices based on imines and the imine:PTB7 composite.

scholarly journals A multi-nuclear magnetic resonance and density functional theory investigation of epitaxially grown InGaP2

2016 ◽  
Vol 18 (31) ◽  
pp. 21296-21304 ◽  
Author(s):  
P. J. Knijn ◽  
P. J. M. van Bentum ◽  
C. M. Fang ◽  
G. J. Bauhuis ◽  
G. A. de Wijs ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Density Functional ◽  
Nmr Spectra ◽  
Functional Theory ◽  
Dft Modelling ◽  
Nuclear Magnetic

NMR spectra of InGaP2, dependent on coordination and disorder. Experimental (left) and DFT modelling (right).

scholarly journals Sulfur Versus Nitrogen Chelation in C-H Activation: Cobalt(III)-Catalyzed Unsymmetrical Double Annulation of Thioamides

2021 ◽  
Author(s):  
Majji Shankar ◽  
Arijit Saha ◽  
Somratan Sau ◽  
Arghadip Ghosh ◽  
Vincent Gandon ◽  
...  
Keyword(s):  
Density Functional ◽  
Chemical Space ◽  
Photophysical Properties ◽  
Structural Diversity ◽  
One Pot ◽  
Functional Theory ◽  
Biologically Relevant ◽  
Drug Candidates ◽  
Isoquinoline Derivatives ◽  
First Time

An unconventional cobalt(III)-catalyzed one-pot domino double annulation of aryl thioamides with unactivated alkynes is presented. Sulfur (S), nitrogen (N), and o,o'-C-H bonds of aryl thioamides are involved in this reaction, enabling access to rare 6,6-fused thiopyrano-isoquinoline derivatives. A reverse ‘S’ coordination over more conventional ‘N’ coordination of thioamides to Co-catalyst specifically regulates the formation of four [C-C and C-S at first and then C-N and C-C] bonds in a single operation, a concept which is uncovered for the first time. The power of the N-masked methyl phenyl sulfoximine (MPS) directing group in this annulation sequence is established. The transformation is successfully developed, building a novel chemical space of structural diversity (56 examples). In addition, late-stage annulation of biologically relevant motifs and drug candidates are disclosed (17 examples). Preliminary photophysical properties of thiopyrano-isoquinoline derivatives are discussed. Density functional theory (DFT) studies authenticate the participation of a unique 6p-electrocyclization of a 7-membered S-chelated cobaltacycle in the annulation process.<br>

scholarly journals Memory-assisted reinforcement learning for diverse molecular de novo design

2020 ◽  
Author(s):  
Thomas Blaschke ◽  
Ola Engkvist ◽  
Jürgen Bajorath ◽  
Hongming Chen
Keyword(s):  
Reinforcement Learning ◽  
De Novo ◽  
Molecular Design ◽  
Chemical Space ◽  
Scoring Function ◽  
Chemical Diversity ◽  
Chemical Structures ◽  
Machine Learning Model ◽  
Low Diversity ◽  
De Novo Molecular Design

Abstract In de novo molecular design, recurrent neural networks (RNN) have been shown to be effective methods for sampling and generating novel chemical structures. Using a technique called reinforcement learning (RL), an RNN can be tuned to target a particular section of chemical space with optimized desirable properties using a scoring function. However, ligands generated by current RL methods so far tend to have relatively low diversity, and sometimes even result in duplicate structures when optimizing towards desired properties. Here, we propose a new method to address the low diversity issue in RL for molecular design. Memory-assisted RL is an extension of the known RL, with the introduction of a so-called memory unit. As proof of concept, we applied our method to generate structures with a desired AlogP value. In a second case study, we applied our method to design ligands for the dopamine type 2 receptor and the 5-hydroxytryptamine type 1A receptor. For both receptors, a machine learning model was developed to predict whether generated molecules were active or not for the receptor. In both case studies, it was found that memory-assisted RL led to the generation of more compounds predicted to be active having higher chemical diversity, thus achieving better coverage of chemical space of known ligands compared to established RL methods.

Theoretical and experimental studies of IR and NMR spectra of gem-2,2-diamino-4,4,6,6-tetraphenoxy-1,3,5-cyclo-triaza-λ5-phosphorine

2010 ◽  
Vol 75 (11) ◽  
pp. 1125-1138
Author(s):  
Lenka Dastychová ◽  
Dalibor Dastych ◽  
Pavel Kubáček ◽  
Milan Alberti
Keyword(s):  
Density Functional ◽  
Nmr Spectra ◽  
Experimental Studies ◽  
Normal Modes ◽  
Chemical Calculation ◽  
Functional Theory ◽  
Calculation Results ◽  
Vibrational Bands ◽  
First Time ◽  
C Nmr

The vibrational spectra of gem-2,2-diamino-4,4,6,6-tetraphenoxy-1,3,5-cyclo-triaza-λ5-phosphorine were studied using density functional theory. Selected vibrational bands were assigned to normal modes on the basis of DFT calculation with the ADF program package. The 1H and 13C NMR spectra, the higher order 31P, 31P{1Ham.(sel.)} and 31P{1Harom.(sel.)} NMR spectra were measured and the values of 1J(C,H), 2J(C,H) and 2J(PI,PII) were found. Nearly the complete spin system (ABB′M4X4X4′) for the symmetry C2 was simulated with the gNMR simulation program and the values of 2J(PI,Ham.), 4J(PII,Ham.), 4J(PII,Harom.), 6J(PI,Harom.) and 6J(PII,H′arom.) were determined for the first time. The experimental NMR data were also compared with quantum chemical calculation results.

scholarly journals Density functional theory: 1H and 13C-NMR spectra of some coumarin derivatives

2014 ◽  
Vol 79 (11) ◽  
pp. 1405-1411 ◽  
Author(s):  
Selma Spirtovic-Halilovic ◽  
Mirsada Salihovic ◽  
Snezana Trifunovic ◽  
Suncica Roca ◽  
Elma Veljovic ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
13C Nmr ◽  
Density Functional ◽  
Nmr Spectra ◽  
Chemical Shifts ◽  
13C Nmr Spectra ◽  
Coumarin Derivatives ◽  
Functional Theory ◽  
1H And 13C Nmr ◽  
Isotropic Chemical Shifts

For some synthesized coumarin derivatives, 1H and 13C NMR isotropic chemical shifts and some other molecular properties were calculated using density functional theory. The calculations yield reliable results, that are in good correlation with experimental data. This is a good basis for the collaboration between experimentalists and quantum chemists.

Structures, Theoretical Vibrational Frequency and 1H-NMR Spectral Analysis of Pyrazine-Dibenzylsulfoxide Platinum(II) Complexes

2011 ◽  
Vol 391-392 ◽  
pp. 1375-1382
Author(s):  
Zheng Ping Wu ◽  
Ian S. Butler
Keyword(s):  
Vibrational Frequency ◽  
Density Functional ◽  
Nmr Spectra ◽  
Mixed Ligand ◽  
High Symmetry ◽  
Dft Methods ◽  
Functional Theory ◽  
H Nmr ◽  
Calculation Results ◽  
Cis And Trans

Mixed-ligand Pt(II) complexes containing pyrazine (C4N2H4, pz) and dibenzyl sulfoxide [C6H5CH2)2SO, DBzSO] ligands have been studied using density functional theory (DFT) methods with a particular emphasis on the theoretical1H-NMR spectra of the methylene protons. The DFT optimization calculations on Pt(DBzSO)Cl2(pz) and {Pt(DBzSO)Cl2}2(pz) predicted the structure parameters, vibrational frequency and1H-NMR spectra. Different structures of DBzSO will affect the bond lengths and angles in the complexes, except for the pz ligands. The [shift(Pt(II)complex)-shift(sulfoxide)] values of trans-Pt(DBzSO)(pz)Cl2were smaller than those for cis-Pt(DBzSO)(pz)Cl2and the calculation results appear to be reasonable. The1H-NMR spectra of the methylene protons of cis- and trans-{Pt(DBzSO)Cl2}2(pz) indicate that these two structures have high symmetry.

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