scholarly journals Investigation of the position of the radical in z3-ions resulting from electron transfer dissociation using infrared ion spectroscopy

2019 ◽  
Vol 217 ◽  
pp. 434-452 ◽  
Author(s):  
Lisanne J. M. Kempkes ◽  
Jonathan Martens ◽  
Giel Berden ◽  
Kas J. Houthuijs ◽  
Jos Oomens
Keyword(s):  
Mass Spectrometry ◽  
Density Functional Theory ◽  
Electron Transfer ◽  
Density Functional ◽  
Electron Transfer Dissociation ◽  
Open Shell ◽  
Molecular Structures ◽  
Functional Theory ◽  
Ion Spectroscopy ◽  
Molecular Dynamics Calculations

The molecular structures of six open-shell z3-ions resulting from electron transfer dissociation mass spectrometry (ETD MS) were investigated using infrared ion spectroscopy in combination with density functional theory and molecular mechanics/molecular dynamics calculations.

Density functional theory for open-shell singlet biradicals

1998 ◽  
Vol 288 (5-6) ◽  
pp. 593-602 ◽  
Author(s):  
Jürgen Gräfenstein ◽  
Elfi Kraka ◽  
Dieter Cremer
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Open Shell ◽  
Functional Theory

Synthesis of urease inhibitory 2, 4-bis (4-cyanobenzyl)glycoluril using sandmeyer reaction and density functional theory investigation

2021 ◽  
Vol 18 ◽  
Author(s):  
Mirza Arfan Yawer ◽  
Shehar Bano ◽  
Muhammad Saleem ◽  
Affiefa Yawer ◽  
Riaz Hussain ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Density Functional Theory ◽  
1H Nmr ◽  
13C Nmr ◽  
Density Functional ◽  
Spectroscopic Techniques ◽  
Pure Compound ◽  
Functional Theory ◽  
Sandmeyer Reaction ◽  
Urease Enzyme

Aims: The aim of present research was to synthesize glycoluril derivative 2,4-Bis(4-cyanobenzyl)glycoluril through convergent scheme. Background: For this purpose Sandmeyer reaction procedure was employed for the synthesis of said compound. The structure of the pure compound was confirmed by using different spectroscopic techniques such as 1H-NMR, 13C-NMR and (HR-MS) Mass spectrometry. Objective: Convergent synthesis of 2,4-BIS (4-CYANOBENZYL)GLYCOLURIL USING SANDMEYER REACTION and urease inhibition study. Methods: The structure of the pure compound was confirmed by using different spectroscopic techniques such as 1H-NMR, 13C-NMR and (HR-MS) Mass spectrometry. The electronic properties of newly synthesized compound and thiourea were determined by using density functional theory. Results: Furthermore compound was evaluated against urease enzyme and was found to be potent inhibitors with IC50 value of 11.5 ± 1.50 µM when compared with standard inhibitor thiourea (IC50 = 21.0 ± 1.90 µM). Compound may serve as lead compound for the synthesis of new cyano based bambusuril in future with enhanced biological properties. Conclusion: We have synthesized a new glycoluril derivative 2,4-Bis(4-cyanobenzyl)glycoluril by the sandmeyer reaction. It has obtained in the form of light yellowish powder in good yield (96%). Glycoluril based macrocycles have been used in various fields. Starting from the 2,4-Bis(4-nitrobenzyl)glycoluril (already reported compound) which has undergone reduction (CH3OH,Pt/C) , diazotization (NaNO2/HCl), cyanation (CuCl/KCN) respectively in order to synthesize the desired new glycoluril derivative. The obtained product will be used as a building block for the synthesis of the cyano based bambusuril marcocycle in future. The yield of the obtained product has been monitored by using different amount of cyanating reagent but the best results shown by the use of 4 mmol of CuCl/KCN. KCN with CuCl assisted the conversion of diazo group into cyano group with enhanced yield when used in excess amount. It act as a catalyst. Solubility characteristic of 2,4-Bis(4-cyanobenzyl)glycoluril has determined also in different organic solvents. 1H NMR technique proved to be very helpful for the structure determination of our desired product. Benzylic protons give signals at 7.5 ppm and 7.8 ppm respectively. The downfield peaks confirm about the presence of CN group near the benzylic protons. Methine protons show signal at 5.2 ppm which ensures about the basic skeleton of glycoluril. Ureidyl protons also confirm the synthesis of the heterocyclic 2,4-Bis(4-cyanobenzyl)glycoluril compound. The negative and positive electrostatic potential sites, molecular descriptors, and charge density distribution of frontier molecular orbitals are revealing that 4a with promising sites for electrophilic and nucleophilic attacks would result to enhance the urease inhbition which is in good agreement with the experimental data.

scholarly journals Including dispersion interactions in the ONETEP program for linear-scaling density functional theory calculations

2008 ◽  
Vol 465 (2103) ◽  
pp. 669-683 ◽  
Author(s):  
Quintin Hill ◽  
Chris-Kriton Skylaris
Keyword(s):  
Density Functional Theory ◽  
Density Functional ◽  
Computational Cost ◽  
Density Functional Theory Calculations ◽  
Binding Energies ◽  
Molecular Structures ◽  
Dispersion Interactions ◽  
Biomolecular Systems ◽  
Functional Theory ◽  
High Level

While density functional theory (DFT) allows accurate quantum mechanical simulations from first principles in molecules and solids, commonly used exchange-correlation density functionals provide a very incomplete description of dispersion interactions. One way to include such interactions is to augment the DFT energy expression by damped London energy expressions. Several variants of this have been developed for this task, which we discuss and compare in this paper. We have implemented these schemes in the ONETEP program, which is capable of DFT calculations with computational cost that increases linearly with the number of atoms. We have optimized all the parameters involved in our implementation of the dispersion correction, with the aim of simulating biomolecular systems. Our tests show that in cases where dispersion interactions are important this approach produces binding energies and molecular structures of a quality comparable with high-level wavefunction-based approaches.

scholarly journals Polydopamine and eumelanin molecular structures investigated with ab initio calculations

2017 ◽  
Vol 8 (2) ◽  
pp. 1631-1641 ◽  
Author(s):  
Chun-Teh Chen ◽  
Francisco J. Martin-Martinez ◽  
Gang Seob Jung ◽  
Markus J. Buehler
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Dft Calculations ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Density Functional ◽  
Md Simulations ◽  
Molecular Structures ◽  
Brute Force ◽  
Functional Theory

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

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