The Low-/Room-temperature Forms Of The Lithiated Salt Of 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone: A Combined Experimental And Dispersion-Corrected Density Functional Study

In press, in CrystEngComm (DOI:10.1039/C2CE26523). This is my first full paper completely internet-powered, in that I’ve not physically met any of the other co-authors (also in the internet-powered context, the recent paper on [18]-annulene was written and submitted without sharing a room with Dr. Bruce Hudson, but we’re in the same building, so it doesn’t quite count). Also, one of the few papers for which I had no image generation duties (a rare treat).

The discussion of the very interesting possibilities of molecular redox materials in lithium-ion batteries aside, this paper presents a very thorough example of the power of computational approaches to greatly improve the understanding of solid-state molecular materials by (specifically) 1: overcoming the hydrogen position identification problems inherent in X-ray diffraction methods, 2: reproducing the changes that come with temperature variations in molecular crystals and explaining the origins of those (possibly subtle) changes by way of dispersion-corrected density functional theory, and 3: demonstrating that the nature of intermolecular interactions (specifically hydrogen bonding) can be rigorously cataloged across varied materials using post-optimization tools (in this case, using Carlo Gatti’s excellent TOPOND program).

2013dec20_crysengcommcover

Caption: Issue cover.

Gaëtan Bonnard, Anne-Lise Barrès, Olivier Mentré, Damian G. Allis, Carlo Gatti, Philippe Poizot and Christine Frayret*

Abstract

Following our first experimental and computational study of the room temperature (RT) form of the tetrahydrated 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone (LiM2DHDMQâ‹…4H2O) compound, we have researched the occurrence of hydrogen ordering in a new polymorph at lower temperature. The study of polymorphism for the Li2DHDMQâ‹…4H2O phase employs both experimental (single crystal X-ray diffraction) and theoretical approaches. While clues for disorder over one bridging water molecule were observed at RT (beta-form),a fully ordered model within a supercell has been evidenced at 100K (alpha-form) and is discussed in conjunction with the features characterizing the first polymorphic form reported previously. Density functional theory (DFT) calculations augmented with an empirical dispersion correction (DFT-D) were applied for the prediction of the structural and chemical bonding properties of the alpha and beta polymorphs of Li2DHDMQ·4H2O. The relative stability of the two polymorphic systems is evidenced. An insight into the interplay of hydrogen bonding, electrostatic and van der Waals (vdW) interactions in affecting the properties of the two polymorphs is gained. This study also shows how information from DFT-D calculations can be used to augment the information from the experimental crystal diffraction pattern and can so play an active role in crystal structure determination, especially by increasing the reliability and accuracy of H-positioning. These more accurate hydrogen coordinates allowed for a quantification of H-bonding strength through a topological analysis of the electron density (Atoms-in-molecules theory).

The Low-Temperature X-ray Structure, Raman and Inelastic Neutron Scattering Vibrational Spectroscopic Investigation of the Non-centrosymmetric Amino Acid Salt Glycine Lithium Sulfate

Accepted in the Journal of Molecular Structure.  A nice article by the official author (M.R.H.) that combines multiple experimental methodologies with quantum chemical simulations using density functional theory to characterize a molecular inorganic solid with constituents known to have interesting ferroelectric and nonlinear optical (NLO) properties.  We can design remarkably complicated molecules and perform rigorous quantum chemical analyses to tailor properties, but the simple molecules still hold the greatest interest to the application-focused experimentalists (something about being able to make them…).

If this were a terahertz spectroscopy (THz) paper, it would serve as yet another shining example of how one cannot perform isolated-molecule calculations for the assignment of vibrational modes (as the molecules in this system, glycine and sulfate, are THz-transparent).  Relevant to inelastic neutron scattering (INS) and optical (infrared and Raman) spectroscopic techniques, the interesting result of the computational analysis is the predicted overestimation of the energy of the vibrational mode corresponding to the rotation of the -NH3+ groups (in the figure below, nitrogen is in blue, oxygen is in red) in the solid-state.

The question to ask: Is this overestimation in the mode energy a result of (a) the solid-state calculations (BLYP/DNP with DMol3) over-predicting the binding energy of the -NH3+ protons to their hydrogen-bonding proton acceptors (sulfate oxygens being the majority acceptor), (b) expansion of the molecules from their crystal geometries such that the hydrogen atoms are pushed closer to their hydrogen-bond acceptors (so the interaction strength and mode energy is artificially increased because the “oscillator” is smaller), or (c) the use of the harmonic approximation to estimate the shape of the potential for the -NH3+ rotor-esque anharmonic motion (which, in these rotors and similar systems (specifically methyl groups), has been generally seen to be an important (if not occasionally singular) explanation)?

The answer is likely all three.

Matthew R. Hudson, Damian G. Allis, Wayne Ouellette, Patrick M. Hakey and Bruce S. Hudson

Department of Chemistry, 1-014 Center for Science and Technology, Syracuse University, Syracuse, NY 13244-4100, USA

Abstract: The structure of the amino acid salt glycine lithium sulfate (GLS) is determined by X-ray diffraction at 90 K and reveals no significant deviations from the previously reported room temperature structure.  The vibrational spectrum of GLS is measured at 78 and 298 K by Raman spectroscopy and at 25 K by incoherent inelastic neutron scattering (INS) spectroscopy. There is no evidence of a phase transition in the Raman spectra between 78 and 298 K.  Solid-state density functional theory (DFT) is used to simulate the INS spectrum of GLS and to perform a complete normal mode analysis.  Discrepancy between simulation and experiment, namely the anharmonic torsional motion of the -NH3+ functional group at approximately 370 cm-1, is discussed in detail.

Keywords: glycinesulfatodilithium, glycine lithium sulfate, inorganic amino acid salt, nonlinear optical material, vibrational spectroscopy, inelastic neutron scattering spectroscopy, solid-state density functional theory

www.elsevier.com/locate/molstruc
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Ferroelectric
en.wikipedia.org/wiki/Nonlinear_optical
en.wikipedia.org/wiki/Time_domain_terahertz_spectroscopy
en.wikipedia.org/wiki/Glycine
en.wikipedia.org/wiki/Sulfate
en.wikipedia.org/wiki/Inelastic_neutron_scattering
en.wikipedia.org/wiki/Infrared
en.wikipedia.org/wiki/Raman_spectroscopy
accelrys.com/products/materials-studio/modules/dmol3.html
en.wikipedia.org/wiki/Hydrogen-bonding
en.wikipedia.org/wiki/Quantum_harmonic_oscillator
chemistry.syr.edu
www.syr.edu