Fingerprinting petroporphyrin structures with vibrational spectroscopy. Part 7. Calculations using density functional theory of the molecular structures and structure-sensitive vibrational modes of type II nickel(II) cycloalkanoporphyrins

In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate the structure of methanesulfonic acid (MSA) in the liquid and solid states. The spectra clearly show that the hydrogen bonding is much stronger in the solid than the liquid state. The structure of MSA is not known; however, mineral acids typically adopt a chain structure in condensed phases. A periodic density functional theory (CASTEP) calculation based on the linear chain structure found in the closely related molecule trifluoromethanesulfonic acid gave good agreement between the observed and calculated spectra, particularly with regard to the methyl and sulfonate groups. The model accounts for the large widths of the asymmetric S-O stretch modes; however, the external mode region is not well described. Together, these observations suggest that the basic model of four molecules in the primitive unit cell, linked by hydrogen bonding into chains, is correct, but that MSA crystallizes in a different space group than that of trifluoromethanesulfonic acid.

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(5656)Macrotetracyclic chelates of doubly charged 3d-element ions with 1,4,8,11-tetraazacyclotetradecane-2,3,9,10-tetrathione and their molecular structures according to density functional theory data

Russian Journal of Inorganic Chemistry ◽

10.1134/s0036023614110138 ◽

2014 ◽

Vol 59 (11) ◽

pp. 1276-1282 ◽

Cited By ~ 10

Author(s):

O. V. Mikhailov ◽

D. V. Chachkov

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Molecular Structures ◽

Functional Theory ◽

Doubly Charged ◽

Density Functional Theory Data

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

Proceedings of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rspa.2008.0398 ◽

2008 ◽

Vol 465 (2103) ◽

pp. 669-683 ◽

Cited By ~ 33

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.

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Polydopamine and eumelanin molecular structures investigated with ab initio calculations

Chemical Science ◽

10.1039/c6sc04692d ◽

2017 ◽

Vol 8 (2) ◽

pp. 1631-1641 ◽

Cited By ~ 67

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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