The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion

Jump to the basis sets and downloadable files here: files, 6-31G, 6-31Gd, 6-31Gdp.

If you use these results: Please drop me a line (damian@somewhereville.com), just to keep track of where this does some good. That said, you should most certainly cite the EMSL and Basis Set references at the bottom of this page.

It’s a fair bet that Sir John Pople would be the world’s most cited researcher by leaps and bounds if people properly cited their use of the basis sets he helped develop.

The full 6-31G, 6-31G(d), and 6-31G(d,p) series (yes, adding 6-31G(d) is a bit of a cheat in this list) from the EMSL Basis Set Exchange is presented here in the interest of giving the general CRYSTALXX (that’s CRYSTAL88, CRYSTAL92, CRYSTAL95, CRYSTAL98, CRYSTAL03, CRYSTAL06, CRYSTAL09, now CRYSTAL14 – providing the names here for those who might be searching by version) user a “standard set” of basis sets that are, for the most part, the same sets one does / could employ in other quantum chemistry codes (with my specific interest being the use and comparison of Gaussian and GAMESS-US in their “molecular” (non-solid-state) implementations). Members of the CRYSTAL developer team provide a number of basis sets for use with the software. While this is good, I will admit that I cannot explain why the developers chose not to include three of the four most famous basis sets in all of (all of) computational chemistry – 3-21G (upcoming), 6-31G(d,p) (presented here), and 6-311G(d,p) (also upcoming).

Continue reading “The EMSL Basis Set Exchange 6-31G, 6-31G(d), And 6-31G(d,p) Gaussian-Type Basis Set For CRYSTAL88/92/95/98/03/06/09/14/etc. – Conversion, Validation With Gaussian09, And Discussion”

Isotopically-Labeled Solid-State Vibrational Mode Energies And Intensities In Crystal09 – A Simple How-To

The generation of isotopically-substituted molecular crystal spectra has become a point of interest, which means blog post. To be clear, this is for cases where isotopic substitution does not affect the crystal geometry – the crystal cell does not change significantly upon deuteration (and for those who believe isotopic substitution never leads to significant changes in the solid, I refer you Zhou, Kye, and Harbison’s article on Isotopomeric Polymprphism and their work on 4-methylpyridine pentachlorophenol, which changes dramatically upon deuteration. I beat on this point because blindly assuming of the crystal cell geometry in such cases will produce spectra noticeably different than measured. It’s NOT the calculation’s fault!).

The generation of isotopically-substituted spectra and intensities in Crystal09 is trivial provided that you KEEP THE FREQINFO.DAT FILE. In fact, you need keep ONLY the FREQINFO.DAT to generate these spectra, which greatly reduces file transfer loads and allows for the scripted calculation of new vibrational spectra and thermodynamic data post-frequency calculation.

Continue reading “Isotopically-Labeled Solid-State Vibrational Mode Energies And Intensities In Crystal09 – A Simple How-To”

Running (Only) A Single-Point Energy Calculation In Crystal06/09, Proper Input Format For Long-Range Dispersion Contributions In Crystal09, And Removing The MPICH2 Content From The Output File In Pcrystal

Now enjoying the benefits of dispersion-corrected solid-state density functional theory (and a proper MPICH2 implementation for infrared intensity calculations, although this now a problem for reasons to be addressed in an upcoming post) in Crystal09, three issues in recent calculations caused me to think hard enough about keyword formats and job runs that I have opted to post briefly about what to do in case google and bing are your preferred methods of manual searching.

1. How To Run Only A Single-Point Energy Calculation In Crystal06/Crystal09

This had never come up before and, by the time I needed to find an input file to see what do to, the first google search provided Civalleri’s Total Energy Calculation page that currently has broken links to .zip files. There is quite a bit about the different geometry optimization approaches in the manual, but a search for “single-point” provides no information about what to do for only single-point energy calculations.

Continue reading “Running (Only) A Single-Point Energy Calculation In Crystal06/09, Proper Input Format For Long-Range Dispersion Contributions In Crystal09, And Removing The MPICH2 Content From The Output File In Pcrystal”

Terahertz Spectroscopic Investigation Of S-(+)-Ketamine Hydrochloride And Vibrational Assignment By Density Functional Theory, “Function Follows Functional Follows Formalism”

Accepted in the Journal of Physical Chemistry A, with my fingers crossed for pulling off the rare double-header in an upcoming print edition of the journal (having missed it by three intermediate articles with the Cs2B12H12 and HMX papers back in 2006 (you’d keep track, too). A fortuitous overlap of scheduled defense dates between P. Hakey, Ph.D. and M. Hudson, A.B.D.). A brief summary of interesting points from this study is provided below, including what I think is a useful point about how to most easily interpret AND represent solid-state vibrational spectra for publications.

1. AS USUAL, YOU CANNOT USE GAS-PHASE CALCULATIONS TO ASSIGN SOLID-STATE TERAHERTZ SPECTRA. It will take a phenomenal piece of data and one helluvan interpretation to convince me otherwise. As a more subtle point (for those attempting an even worse job of vibrational mode assignment), if the molecule exists in its protonated form in the solid-state, do not use the neutral form for your gas-phase calculation (this is a point that came up as part of an MDMA re-assignment published (and posted here) previously).

2. It is very difficult to find what I would consider to be “complete data sets” for molecules and solids being studied by spectroscopic and computational methods. For many molecular solids, the influences of thermal motion are not important to providing a proper vibrational analysis by solid-state density functional theory methods. Heating a crystal may make spectral lines broader, but phase changes and unusual spectral features do not often result when heating a sample from cryogenic (say, liquid nitrogen) to room temperature. Yes, there are thousands of cases where this is not true, but several fold more cases where it is. We are fortunate to live in a temperature regime where characterization is reasonably straightforward and yet we can modify a system to observe its subtle changes under standard laboratory conditions. The THz spectrum of S-(+)-Ketamine Hydrochloride gets a bit cleaner upon cooling, which makes the assignment easier. As the ultimate goal is to be able to characterize these systems in a person’s pocket instead of their liquid nitrogen thermos, the limited observed change to the spectrum upon cooling is important to note.

3. Crystal06 vs. DMol3 – This paper contains what is hoped to be a level, pragmatic discussion about the strengths and weaknesses of computational tools available to terahertz spectroscopists for use in their efforts to assign spectra. This type of discussion is, as a computational chemist using tools and not developing tools, a touchy subject to present on not because of the finger-pointing of limitations with software, but because the Crystal06 team and Accelrys (through Delley’s initial DMol3 code) clearly are doing things that the vast majority of their users (myself included) could in no way do by themselves. The analysis for the theory-minded terahertz spectroscopist is presented comparing two metrics – speed and functionality (specifically, infra-red intensity prediction). What is observed as the baseline is that both DMol3 and Crystal06 make available density functionals and basis sets that, when used at high levels of theory and rigorous convergence criteria, produce simulated terahertz spectra with vibrational mode energies that are in good (if not very good) agreement with each other. For the terahertz spectroscopist, Crystal06 provides as output (although this is system size- and basis set size-dependent) rigorous infrared intensity predictions for vibrational modes, inseparable from mode energy as “the most important” pieces of information for mode assignments. While DMol3 does not produce infrared intensities (the many previous terahertz papers I’ve worked on employed difference-dipole calculations that are, at best, a guesstimate), DMol3 produces very good mode energy predictions in 1/6th to (I’ve seen it happen) 1/10th the time of a comparable Crystal06 calculation. This is the reason DMol3 has been the go-to program for all of the neutron scattering spectroscopy papers cited on this blog (where intensity is determined by normal mode eigenvectors, which are provided by both (and any self-respecting quantum chemical code) programs).

Now, it should be noted that this difference in functionality has NOTHING to do with formalism. Both codes are excellent for what they are intended to do. To the general assignment-minded spectroscopist (the target audience of the Discussion in the paper), any major problem with Crystal06 likely originates with the time to run calculations (and, quite frankly, the time it takes to run a calculation is the worst possible reason for not running a calculation if you need that data. Don’t blame the theory, blame the deadline). In my past exchanges with George Fitzgerald of Accelrys, the issue of DMol3 infrared intensities came up as a feature request that would greatly improve the (this) user experience and Dr. Fitzgerald is very interested (of course) in making a great code that much better. Neither code will be disappearing from my toolbox anytime soon.

4. The Periodicity Of The Molecular Solid Doesn’t Care What The Space Group Is – One of the more significant problems facing the assignment-minded spectroscopist is the physical description of molecular motion in a vibrational mode. In the simplest motions involving the most weakly interacting molecules, translational and rotational motions are often quite easy to pick out and state as such. When the molecules are very weakly interacting, often the intramolecular vibrational modes are easy to identify as well, as they are largely unchanged from their gas-phase descriptions. In ionic solids or strongly hydrogen-bonded systems, it is often much harder to separate out individual molecular motions from “group modes” involving the in- and out-of-phase motions of multiple molecules. In the unit cells of molecular solids, it can be the case that these group modes appear, by inspection, to be extremely complicated, sometimes too involved to easily describe in the confines of a table in a journal article.

S-(+)-Ketamine Hydrochloride is one such example where a great simplification in vibrational mode description comes from thinking, well, “outside the box.” The image below shows two cells and the surrounding molecules of S-(+)-Ketamine Hydrochloride. As it is difficult to see why the mode descriptions are complex from just an image, assume that I am right in this statement of complexity. Part of this complexity comes from the fact that the two molecules in the unit cell are not strongly interacting, instead packed together by van der Waals and dispersion forces more than anything else. The key to a greatly simplified assignment comes from the realization that the most polar fragments of these molecules are aligned on the edges of the unit cell.

An alternate view of molecular vibrational motion comes from considering not the contents of the defined unit cell but the hydrogen-bonding and ionic bonding arrangement that exists between pairs of molecules between unit cells. The colorized image below shows two distinct chains (red and blue) that, when the predicted vibrational modes are animated, become trivial to characterize as the relative motions of a hydrogen/ionic-bonded chain. Rotational motions appear as spinning motions of the chains, translational motions as either chain sliding motions or chain breathing modes. It appears as a larger macromolecule undergoing very “molecular” vibrations. In optical vibrational spectroscopy, selection rules and the unit cell arrangement do not produce in- and out-of-phase motions of the red and blue chains, as only one “chain” exists in the periodicity of the unit cell. In neutron scattering spectroscopy, these relative motions between red and blue would appear in the phonon region. This same discussion was had, in part, in a previous post on the solid-state terahertz assignment of ephedrine (with a nicer picture).

So, look at the cell contents, then see if there’s more structure than crystal packing would indicate. It greatly simplifies the assignment (which, in turn. greatly simplifies the reader’s digestion of the vibrational motions).

Patrick M. Hakey, Damian G. Allis, Matthew R. Hudson, Wayne Ouellette, and Timothy M. Korter

Department of Chemistry, Syracuse University, Syracuse, New York 13244-4100

Abstract: The terahertz (THz) spectrum of (S)-(+)-ketamine hydrochloride has been investigated from 10 to 100 cm-1 (0.3-3.0 THz) at both liquid-nitrogen (78 K) and room (294 K) temperatures. Complete solid-state density functional theory structural analyses and normal-mode analyses are performed using a single hybrid density functional (B3LYP) and three generalized gradient approximation density functionals (BLYP, PBE, PW91). An assignment of the eight features present in the well-resolved cryogenic spectrum is provided based upon solid-state predictions at a PW91/6-31G(d,p) level of theory. The simulations predict that a total of 13 infrared- active vibrational modes contribute to the THz spectrum with 26.4% of the spectral intensity originating from external lattice vibrations.

pubs.acs.org/journal/jpcafh
www.somewhereville.com/?p=29
www.somewhereville.com/?p=26
www.somewhereville.com/?p=126
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Ketamine
www.crystal.unito.it
accelrys.com/products/materials-studio/quantum-and-catalysis-software.html
en.wikipedia.org/wiki/Time_domain_terahertz_spectroscopy
en.wikipedia.org/wiki/Computational_chemistry
accelrys.com
en.wikipedia.org/wiki/Inelastic_neutron_scattering
en.wikipedia.org/wiki/Vibrational_spectroscopy
www.somewhereville.com/?p=680

The Vibrational Spectrum Of Parabanic Acid By Inelastic Neutron Scattering Spectroscopy And Simulation By Solid-State DFT

Available as an ASAP in The Journal of Physical Chemistry A. As a general rule in computational chemistry, the smaller the molecule, the harder it is to get right. As a brief summary, parabanic acid has several interesting properties of significance to computational chemists as both a model for other systems containing similar sub-structures and as a complicated little molecule in its own right.

1. The solid-state spectrum requires solid-state modeling. This should be of no surprise (see the figure below for the difference in solid-state (top) and isolated-molecule (bottom)). This task was undertaken with both DMol3 and Crystal06, with DMol3 calculations responsible for the majority of the analysis of this system (as has always been the case in the neutron studies reported on this site).

2. The agreement in the hydrogen-bonded N-H…O vibrations is, starting from the crystal structure, in poor agreement with experiment. You’ll note the region between 750 and 900 cm-1 is a little too high (and for clarification, the simulated spectrum is in red below). According to the kitchen sink that Matt threw at the structure, the problem is not the same anharmonicity one would acknowledge by Dr. Walnut’s “catalytic handwaving” approach to spectrum assignment (Dr. Walnut does not engage in this behavior, rather endeavors to find it in others where it should not be).

3. The local geometry of the hydrogen-bonding network in this molecular solid leads to notable changes in parabanic acid structure that, in turn, leads to the different behavior of the N-H…O vibrational motions. There is one potentially inflammatory comment in the Conclusions section that results from this identification. The parabanic acid molecule is, at its sub-structure, a set of three constrained peptide linkages that under go subtle but vibrationally-observable changes to their geometry because of crystal packing and intermolecular hydrogen bond formation. This means that the isolated molecule and solid-state forms are different and that peptide groups are influenced by neighboring interactions.

So, why should one care? Suppose one is parameterizing a biomolecular force field (CHARMM, AMBER, GROMOS, etc.) using bond lengths, bond angles, etc., for the amino acid geometry and vibrational data for some aspect of the force constant analysis. The structural data for these force fields often originates with solid-state studies (diffraction results). This means, to those very concerned with structural accuracy, that a geometry we know to be influenced by solid-state interactions is being used as the basis for molecular dynamics calculations that will NOT be used in their solid-state forms. Coupled with the different spectral properties due to intermolecular interactions, the description being used as the basis for the biomolecular force field likely being used in solution (solvent box approaches) is based on data in a phase where the structure and dynamics are altered from their less conformationally-restricted counterpart (in this case, solid-state).

A subtle point, but that’s where applied theoreticians do some of their best work.

Matthew R. Hudson, Damian G. Allis, and Bruce S. Hudson

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

Abstract: The incoherent inelastic neutron scattering spectrum of parabanic acid was measured and simulated using solid-state density functional theory (DFT). This molecule was previously the subject of low-temperature X-ray and neutron diffraction studies. While the simulated spectra from several density functionals account for relative intensities and factor group splitting regardless of functional choice, the hydrogen-bending vibrational energies for the out-of-plane modes are poorly described by all methods. The disagreement between calculated and observed out-of-plane hydrogen bending mode energies is examined along with geometry optimization differences of bond lengths, bond angles, and hydrogen-bonding interactions for different functionals. Neutron diffraction suggests nearly symmetric hydrogen atom positions in the crystalline solid for both heavy-atom and N-H bond distances but different hydrogen-bonding angles. The spectroscopic results suggest a significant factor group splitting for the out-of-plane bending motions associated with the hydrogen atoms (N-H) for both the symmetric and asymmetric bending modes, as is also supported by DFT simulations. The differences between the quality of the crystallographic and spectroscopic simulations by isolated-molecule DFT, cluster-based DFT (that account for only the hydrogen-bonding interactions around a single molecule), and solid-state DFT are considered in detail, with parabanic acid serving as an excellent case study due to its small size and the availability of high-quality structure data. These calculations show that hydrogen bonding results in a change in the bond distances and bond angles of parabanic acid from the free molecule values.

pubs.acs.org/doi/abs/10.1021/jp9114095
pubs.acs.org/journal/jpcafh
en.wikipedia.org/wiki/Computational_chemistry
accelrys.com/products/materials-studio/quantum-and-catalysis-software.html
www.crystal.unito.it
en.wikipedia.org/wiki/Anharmonicity
chemistry.syr.edu/faculty/walnut.html
en.wikipedia.org/wiki/Hydrogen_bond
en.wikipedia.org/wiki/Peptide
en.wikipedia.org/wiki/Force_field_%28chemistry%29
www.charmm.org
ambermd.org
gromacs.org
en.wikipedia.org/wiki/Molecular_dynamics

Examination of Phencyclidine Hydrochloride via Cryogenic Terahertz Spectroscopy, Solid-State Density Functional Theory, and X-Ray Diffraction

“I’m high on life… and PCP.” – Mitch Hedberg

In press, in the Journal of Physical Chemistry A. If the current rosters of pending manuscripts and calculations are any indication, this PCP paper will mark the near end of my use of DMol3 for the prediction (and experimental assignment) of terahertz (THz) spectra (that said, it is still an excellent tool for neutron scattering spectroscopy and is part of several upcoming papers).

While the DMol3 vibrational energy (frequency) predictions are generally in good agreement with experiment (among several density functionals, including the BLYP, BOP,VWN-BP, and BP generalized gradient approximation density functionals), the use of the difference-dipole method for the calculation of infrared intensities has shown itself to be of questionable applicability when the systems being simulated are charged (either molecular salts (such as PCP.HCl) or zwitterions (such as the many amino acid crystal structures)). The previously posted ephedrine paper (in ChemPhysChem) is most interesting from a methodological perspective for the phenomenal agreement in both mode energies AND predicted intensities obtained using Crystal06, another solid-state density functional theory program (that has implemented hybrid density functionals, Gaussian-type basis sets, cell parameter optimization and, of course, a more theoretically sound prediction of infrared intensities by way of Born charges). The Crystal06 calculations take, on average, an order of magnitude longer to run than the comparable DMol3 calculations, but the slight additional gain in accuracy for good density functionals, the much greater uniformity of mode energy predictions across multiple density functionals (when multiple density functionals are tested), and the proper calculation of infrared intensities all lead to Crystal06 being the new standard for THz simulations.

After a discussion with a crystallographer about what theoreticians trust and what they don’t in a diffraction experiment, the topic of interatomic separation agreement between theory and experiment came up in the PCP.HCl analysis performed here (wasn’t Wayne). As the position of hydrogen atoms in an X-ray diffraction experiment are categorically one of those pieces of information solid-state theoreticians do NOT trust when presented with a cif file, I reproduce a snippet from the paper considering this difference below (and, generally, one will not find comparisons of crystallographically-determined hydrogen positions and calculated hydrogen positions in any of the THz or inelastic neutron scattering spectroscopy papers found on this blog).

The average calculated distance between the proton and the Cl ion is 2.0148 Angstroms, an underestimation of nearly 0.13 Angstroms when compared to the experimental data. This deviation is likely strongly tied to the uncertainly in the proton position as determined by the X-ray diffraction experiment and is, therefore, not used as a proper metric of agreement between theory and experiment. The distance from the nitrogen atom to the Cl ion has been determined to be an average of 3.0795 Angstroms, which is within 0.002 Angstroms of the experimentally determined bond length. This proper comparison of heavy atom positions between theory and experiment indicates that this interatomic separation has been very well predicted by the calculations.

Patrick M. Hakey, Matthew R. Hudson, Damian G. Allis, Wayne Ouellette, and Timothy M. Korter

Department of Chemistry, Syracuse University, Syracuse, NY 13244-4100

The terahertz (THz) spectrum of phencyclidine hydrochloride from 7.0 – 100.0 cm-1 has been measured at cryogenic (78 K) temperature. The complete structural analysis and vibrational assignment of the compound have been performed employing solid-state density functional theory utilizing eight generalized gradient approximation density functionals and both solid-state and isolated-molecule methods. The structural results and the simulated spectra display the substantial improvement obtained by using solid-state simulations to accurately assign and interpret solid-state THz spectra. A complete assignment of the spectral features in the measured THz spectrum has been completed at a VWN-BP/DNP level of theory, with the VWN-BP density functional providing the best-fit solid-state simulation of the experimentally observed spectrum. The cryogenic THz spectrum contains eight spectral features that, at the VWN-BP/DNP level, consist of fifteen infrared-active vibrational modes. Of the calculated modes, external crystal vibrations are predicted to account for 42% of the total spectral intensity.

en.wikipedia.org/wiki/Mitch_Hedberg
pubs.acs.org/journal/jpcafh
en.wikipedia.org/wiki/Phencyclidine
accelrys.com/products/materials-studio/modules/dmol3.html
en.wikipedia.org/wiki/Terahertz_radiation
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Density_functional_theory#Approximations_.28Exchange-correlation_functionals.29
en.wikipedia.org/wiki/Zwitterions
en.wikipedia.org/wiki/Amino_acid
www.somewhereville.com/?p=680
www3.interscience.wiley.com/journal/122540399/abstract
www.crystal.unito.it
en.wikipedia.org/wiki/Basis_set_(chemistry)
en.wikipedia.org/wiki/X-ray_scattering_techniques
en.wikipedia.org/wiki/Inelastic_neutron_scattering
chemistry.syr.edu
www.syr.edu

Investigation of Crystalline 2-Pyridone Using Terahertz Spectroscopy and Solid-State Density Functional Theory

Accepted in Chemical Physics Letters. A solid-state density functional theory (DFT) follow-up to the solution-phase 2-pyridone (2PD) study published by Motley and Korter previously. Much of the work-up for this paper was straightforward, run-of-the-mill calculation and correlation (on the theory side, anyway). The most difficult part of the analysis was the identification of the easiest way to present the normal mode analysis of the 2PD crystal cell.

In terahertz (THz) spectroscopy, one observes the lowest-frequency vibrational motions of molecules (if the molecule has low-lying vibrational modes, of course). In the solid-state (such as molecular crystals), one observes both low-lying molecular vibrational motions (if they exist) and the relative motions between molecules in the unit cell. The boilerplate separation of internal (intramolecular) and external (between-molecule) modes is performed (and presented) as follows:

A crystal unit cell containing M molecules with N atoms contains 3N-6M internal modes (those modes associated with intramolecular motions), 6M-3 external modes (those modes associated with relative motions between the M molecules, such as rotations and translations), and three acoustic modes.

Some molecules simply do not absorb in the THz region, so all assignments are for external motions (and one simply identifies molecules sliding along axes or spinning around their centers of mass in their lattice site). Some molecules are very strongly bound to neighboring molecules in their lattice sites, which results in significant changes to the mode energies of low-lying vibrational modes (these are far more complicated systems to perform assignments of and a few of these cases are being prepared for future publications). Some molecules are strongly bound in very localized ways in their crystal cell to neighboring molecules and are very weakly bound to other neighbors in other ways. In 2PD, chains of molecules are strongly bound through hydrogen bonding along the crystal c-axis (see the figure below) and only weakly interacting between chains. In the figure below, the blue and red chains are strongly coupled in-chain (hydrogen-bonding) and only weakly coupled (dispersion and van der Waals forces) between chains.

The assignment of the 2PD solid is simplified by two important facts. First, the two chains (red and blue) are related by symmetry (the unit cell contains two anti-parallel 2PD chains). Second, the chains are very weakly interacting.

What point 1 means is that the chains, if in isolation, would undergo the same vibrational motions at the same energies (as if the chains were simply chiral molecules).

What point 2 means is that these chains are, because they interact very weakly, approaching a limit where there can, in fact, be considered isolated chains so that the unit cell will contain vibrational motions that involve the two chains undergoing the same motion in-phase with respect to reach other (in-phase here meaning that, for instance, both of your lungs are expanding at the same time) and out-of-phase with respect each other (the hypothetical case where the left and right lobes are out-of-sync with one another).

For instance, if both chains are sliding along the crystal c-axis in a vibrational mode, that makes the mode the in-phase acoustic translation in c (because the whole cell is sliding in one direction). If the two chains are sliding in opposite directions with respect to each other, this makes the mode the optical translation in c (the center of mass of the cell stays put while the chains undergo out-of-phase motions).

This simplification for the 2PD assignment (and other solid-state molecular chains) turned out to be the mode assignment based on the treatment of not the in-cell contents of atoms and molecular fragments (if we kept ourselves to only viewing what is happening in the cell, for instance), but instead the relative motions of the chains, which requires ever-so-slightly thinking outside of the box.

Tanieka L. Motley, Damian G. Allis, and Timothy M. Korter*

Department of Chemistry, Syracuse University, Syracuse, NY 13244-4100

Crystalline 2-pyridone has been investigated using terahertz vibrational spectroscopy in the range of 10 to 90 cm-1 (0.3 to 2.7 THz). Solid-state density functional theory (B3LYP, BP, and PW91 with the 6-311G(d,p) basis set) was used to simulate and assign both observed terahertz spectral features and a previously published far-infrared spectrum up to 400 cm-1. The PW91 functional was found to provide the best combination of crystal structure and vibrational frequency reproduction. Observed spectral features below 150 cm-1 are assigned to intermolecular movements of the 2-pyridone chains within the unit cell. The use of independent intramolecular and intermolecular frequency scalars is proposed.

www.sciencedirect.com/science/journal/00092614
dx.doi.org/10.1016/j.cplett.2008.09.021
en.wikipedia.org/wiki/2-Pyridone
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Terahertz
en.wikipedia.org/wiki/Vibrational_spectroscopy
en.wikipedia.org/wiki/Hydrogen_bonds
en.wikipedia.org/wiki/Van_der_Waals_force
en.wikipedia.org/wiki/Chirality_(chemistry)
en.wikipedia.org/wiki/Phonon

An Investigation of (1R,2S)-(-)-Ephedrine Using Solid-State Density Functional Theory and Cryogenic Terahertz Spectroscopy

Accepted in ChemPhysChem. Two important points. First, as shown in the crystal cell figure below, the low-frequency study of the ephedrine molecular solid is one that is best considered in the context of two infinite chains (red and blue) that are strongly interacting along the chain and very weakly interacting between chains. The key point is the realization that the ephedrine molecular solid is not best considered as four molecules packed into a crystal cell. The original round of mode assignments, based only in crystal cell contents, was a very complicated list of relative motions and nearly irreconcilable collisions of in- and out-of-phase motions. Thinking outside-the-unit-cell and realizing that the mode motions could be described far more easily (and logically) as chains instead of packed molecules made the final assignment and analysis of the terahertz spectrum very straightforward. The lesson is to take a good look at your molecular solid before attempting to describe the motions and consider divide-and-conquer approaches if you see correlations.

The second reason I am specifically pleased with this paper is that it is the first real terahertz study using Crystal06 that employs multiple generalized gradient approximation density functionals (BP, PBE, PW91) and basis sets (6-31G(d,p) and 6-311G(d,p)) and shows that these multiple levels of theory provide very similar results. That has, generally, NOT been the case with the many previous DMol3 studies that required difference-dipole intensity calculations instead of the use of more rigorous Wannier function-based intensities possible within the Crystal06 code.

Patrick M. Hakey, Damian G. Allis, Matthew R. Hudson, Wayne Ouellette, and Timothy M. Korter

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

Abstract: The terahertz (THz) spectrum of (1R,2S)-(-)-ephedrine from 8.0 to 100.0 cm-1 has been investigated at liquid-nitrogen (78.4 K) temperature. A complete structural analysis has been performed in conjunction with a vibrational assignment of the experimental spectrum using solid-state density functional theory (DFT). In order to obtain the crystallographic lattice constants at a temperature relevant for the DFT simulations, the compound has also been characterized by cryogenic single-crystal X-ray diffraction. Theoretical modeling (solid-state and isolated-molecule) of the compound includes the use of three generalized gradient approximation density functionals (BP, PBE, PW91) and two Gaussian-type basis sets (6-31G(d,p) and 6-311G(d,p)). Assignment of the THz spectrum is performed at a PW91/6-311G(d,p) level of theory, which provides the best solid-state simulation agreement with experiment. The solid-state analysis indicates that the seven experimental spectral features observed at liquid-nitrogen temperature are comprised of 13 IR-active vibrational modes. Of these modes, nine are external crystal vibrations and provide approximately 57% of the predicted spectral intensity.

www3.interscience.wiley.com/journal/72514732/home?CRETRY=1&SRETRY=0
en.wikipedia.org/wiki/Ephedrine
en.wikipedia.org/wiki/Terahertz
www.crystal.unito.it/
en.wikipedia.org/wiki/Density_functional_theory
en.wikipedia.org/wiki/Basis_set_(chemistry)
accelrys.com/products/materials-studio/modules/dmol3.html
en.wikipedia.org/wiki/Wannier_function
chemistry.syr.edu
www.syr.edu

Crystal06 (v.1.0.2) And MPICH-1.2.7p1 In Ubuntu Desktop 8.10 (and 9.04, 64- and 32-bit) Using The Intel Fortran Compiler, Version 1.0

Update 19 May 2009 – This tutorial (and all subsequent modifications) are now on a separate page on this website and will not be modified further in this post.  This page is available HERE.  The forever-name PDF version of the tutorial is available here: crystal06_mpich_ubuntu_cluster.pdf

Pre-19 May 2009 – This document, the end of a very long and involved process, is available as a PDF download (for reading and printing ease) here: crystal06_mpich_ubuntu_cluster_V1.pdf

Introduction

According the Crystal06 manual:

The CRYSTAL package performs ab initio calculations of the ground state energy, energy gradient, electronic wave function and properties of periodic systems. Hartree-Fock or Kohn-Sham Hamiltonians (that adopt an Exchange- Correlation potential following the postulates of Density-Functional theory) can be used. Systems periodic in 0 (molecules, 0D), 1 (polymers, 1D), 2 (slabs, 2D), and 3 dimensions (crystals, 3D) are treated on an equal footing. In each case the fundamental approximation made is the expansion of the single particle wave functions (‘Crystalline Orbital’, CO) as a linear combination of Bloch functions (BF) defined in terms of local functions (hereafter indicated as ‘Atomic Orbitals’, AOs).

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