Category Archives: Quantum Mechanics
This is a guest post by our very own Gustavo “Gus” Mondragón whose work centers around the study of excited states chemistry of photosynthetic pigments.
When you’re calculating excited states (no matter the method you’re using, TD-DFT, CI-S(D), EOM-CCS(D)) the analysis of the orbital contributions to electronic transitions poses a challenge. In this post, I’m gonna guide you through the CI-singles excited states calculation and the analysis of the electronic transitions.
I’ll use adenine molecule for this post. After doing the corresponding geometry optimization by the method of your choice, you can do the excited states calculation. For this, I’ll use two methods: CI-Singles and TD-DFT.
The route section for the CI-Singles calculation looks as follows:
#p CIS(NStates=10,singlets)/6-31G(d,p) geom=check guess=read scrf=(cpcm,solvent=water)
adenine excited states with CI-Singles method
I use the same geometry from the optimization step, and I request only for 10 singlet excited states. The CPCP implicit solvation model (solvent=water) is requested. If you want to do TD-DFT, the route section should look as follows:
#p FUNCTIONAL/6-31G(d,p) TD(NStates=10,singlets) geom=check guess=read scrf=(cpcm,solvent=water)
adenine excited states with CI-Singles method
Where FUNCTIONAL is the DFT exchange-correlation functional of your choice. Here I strictly not recommend using B3LYP, but CAM-B3LYP is a noble choice to start.
Both calculations give to us the excited states information: excitation energy, oscillator strength (as f value), excitation wavelength and multiplicity:
Excitation energies and oscillator strengths:
Excited State 1: Singlet-A 6.3258 eV 196.00 nm f=0.4830 <S**2>=0.000
11 -> 39 -0.00130
11 -> 42 -0.00129
11 -> 43 0.00104
11 -> 44 -0.00256
11 -> 48 0.00129
11 -> 49 0.00307
11 -> 52 -0.00181
11 -> 53 0.00100
11 -> 57 -0.00167
11 -> 59 0.00152
11 -> 65 0.00177
The data below corresponds to all the electron transitions involved in this excited state. I have to cut all the electron transitions because there are a lot of them for all excited states. If you have done excited states calculations before, you realize that the HOMO-LUMO transition is always an important one, but not the only one to be considered. Here is when we calculate the Natural Transition Orbitals (NTO), by these orbitals we can analyze the electron transitions.
For the example, I’ll show you first the HOMO-LUMO transition in the first excited state of adenine. It appears in the long list as follows:
35 -> 36 0.65024
The 0.65024 value corresponds to the transition amplitude, but it doesn’t mean anything for excited state analysis. We must calculate the NTOs of an excited state from a new Gaussian input file, requesting from the checkpoint file we used to calculate excited states. The file looks as follows:
#p SP geom=allcheck guess=(read,only) density=(Check,Transition=1) pop=(minimal,NTO,SaveNTO)
I want to say some important things right here for this last file. See that no level of theory is needed, all the calculation data is requested from the checkpoint file “adenine.chk”, and saved into the new checkpoint file “adNTO1.chk”, we must use the previous calculated density and specify the transition of interest, it means the excited state we want to analyze. As we don’t need to specify charge, multiplicity or even the comment line, this file finishes really fast.
After doing this last calculation, we use the new checkpoint file “adNTO1.chk” and we format it:
formchk -3 adNTO1.chk adNTO1.fchk
If we open this formatted checkpoint file with GaussView, chemcraft or the visualizer you want, we will see something interesting by watching he MOs diagram, as follows:
We can realize that frontier orbitals shows the same value of 0.88135, which means the real transition contribution to the first excited state. As these orbitals are contributing the most, we can plot them by using the cubegen routine:
cubegen 0 mo=homo adNTO1.fchk adHOMO.cub 0 h
This last command line is for plotting the equivalent as the HOMO orbital. If we want to plot he LUMO, just change the “homo” keyword for “lumo”, it doesn’t matter if it is written with capital letters or not.
You must realize that the Natural Transition Orbitals are quite different from Molecular Orbitals. For visual comparisson, I’ve printed also the molecular orbitals, given from the optimization and from excited states calculations, without calculating NTOs:
These are the molecular frontier orbitals, plotted with Chimera with 0.02 as the isovalue for both phase spaces:
The frontier NTOs look qualitatively the same, but that’s not necessarily always the case:
If we analyze these NTOs on a hole-electron model, the HOMO refers to the hole space and the LUMO refers to the electron space.
Maybe both orbitals look the same, but both frontier orbitals are quite different between them, and these last orbitals are the ones implied on first excited state of adenine. The electron transition will be reported as follows:
If I can do a graphic summary for this topic, it will be the next one:
NTOs analysis is useful no matter if you calculate excited states by using CIS(D), EOM-CCS(D), TD-DFT, CASSCF, or any of the excited states method of your election. These NTOs are useful for population analysis in excited states, but these calculations require another software, MultiWFN is an open-source code that allows you to do this analysis, and another one is called TheoDORE, which we’ll cover in a later post.
The video below is a sad recount of the scientific conditions in Mexico that have driven an enormous amount of brain power to other countries. Doing science is always a hard endeavour but in developing countries is also filled with so many hurdles that it makes you wonder if it is all worth the constant frustration.
That is why I think it is even more important for the Latin American community to make our science visible, and special issues like this one from the International Journal of Quantum Chemistry goes a long way in doing so. This is not the first time IJQC devotes a special issue to the Comp.Chem. done south of the proverbial border, a full issue devoted to the Mexican Physical Chemistry Meetings (RMFQT) was also published six years ago.
I believe these special issues in mainstream journals are great ways of promoting our work in a collected way that stresses our particular lines of research instead of having them spread a number of journals. Also, and I may be ostracized for this, but I think coming up with a new journal for a specific geographical community represents a lot of effort that takes an enormous amount of time to take off and thus gain visibility.
For these reasons I’ve been cooking up some ideas for the next RMFQT website. I don’t pretend to say that my colleagues need any shoutouts from my part -I could only be so lucky to produce such fine pieces of research myself- but it wouldn’t hurt to have a more established online presence as a community.
¡Viva la ciencia Latinoamericana!
The concept of electronic orbital has become such a useful and engraved tool in understanding chemical structure and reactivity that it has almost become one of those things whose original meaning has been lost and replaced for a utilitarian concept, one which is not bad in itself but that may lead to some wrong conclusions when certain fundamental facts are overlooked.
Last week a wrote -what I thought was- a humorous post on this topic because a couple of weeks ago a viewpoint in JPC-A was published by Pham and Gordon on the possibility of observing molecular orbitals through microscopy methods, which elicited a ‘seriously? again?‘ reaction from me, since I distinctly remember the Nature article by Zuo from the year 2000 when I just had entered graduate school. The article is titled “direct observation of d-orbital holes.” We discussed this paper in class and the discussion it prompted was very interesting at various levels: for starters, the allegedly observed d-orbital was strikingly similar to a dz2, which we had learned in class (thanks, prof. Carlos Amador!) that is actually a linear combination of d(z2-x2) and d(z2-y2) orbitals, a mathematical -lets say- trick to conform to spectroscopic observations.
Pham and Gordon are pretty clear in their first paragraph: “The wave function amplitude Ψ*Ψ is interpreted as the probability density. All observable atomic or molecular properties are determined by the probability and a corresponding quantum mechanical operator, not by the wave function itself. Wave functions, even exact wave functions, are not observables.” There is even another problem, about which I wrote a post long time ago: orbitals are non-unique, this means that I could get a set of orbitals by solving the Schrödinger equation for any given molecule and then perform a unit transformation on them (such as renormalizing them, re-orthonormalizing them to get a localized version, or even hybridizing them) and the electronic density derived from them would be the same! In quantum mechanical terms this means that the probability density associated with the wave function internal product, Ψ*Ψ, is not changed upon unit transformations; why then would a specific version be “observed” under a microscope? As Pham and Gordon state more eloquently it has to do with the Density of States (DOS) rather than with the orbitals. Furthermore, an orbital, or more precisely a spinorbital, is conveniently (in math terms) separated into a radial, an angular and a spin component R(r)Ylm(θ,φ)σ(α,β) with the angular part given by the spherical harmonic functions Ylm(θ,φ), which in turn -when plotted in spherical coordinates- create the famous lobes we all chemists know and love. Zuo’s observation claim was based on the resemblance of the observed density to the angular part of an atomic orbital. Another thing, orbitals have phases, no experimental observation claims to have resolved those.
Now, I may be entering a dangerous comparison but, can you observe a 2? If you say you just did, well, that “2” is just a symbol used to represent a quantity: two, the cardinality of a set containing two elements. You might as well depict such quantity as “II” or “⋅⋅” but still cannot observe “a two”. (If any mathematician is reading this, please, be gentle.) I know a number and a function are different, sorry if I’m just rambling here and overextending a metaphor.
Pretending to having observed an orbital through direct experimental methods is to neglect the Born interpretation of the wave function, Heisenberg’s uncertainty principle and even Schrödinger’s cat! (I know, I know, Schrödinger came up with this gedankenexperiment in order to refute the Copenhagen interpretation of quantum mechanics, but it seems like after all the cat is still not out of the box!)
So, the take home message from the viewpoint in JPC is that molecular properties are defined by the expected values of a given wave function for a specific quantum mechanical operator of the property under investigation and not from the wave function itself. Wave functions are not observables and although some imaging techniques seem to accomplish a formidable task the physical impossibility hints to a misinterpretation of facts.
I think I’ll write more about this in a future post but for now, my take home message is to keep in mind that orbitals are wave functions and therefore are not more observable (as in imaging) than a partition function is in statistical mechanics.
It is with great pride that I’d like to announce that for the first time we have a Masters Student graduated from this Comp.Chem. lab: María Eugenia “Maru” Sandoval-Salinas has finished her graduate studies and just last Friday defended her thesis admirably earning not only the degree of Masters of Science in Chemistry but doing so with the highest honors given by the National Autonomous University of Mexico.
Maru’s thesis is for many reasons a landmark in this lab not only because it is the first graduate thesis published from our lab but also the first document on our work about the study of Photosynthesis, a long sought after endeavor now closer to publication. It must also be said that Maru came to this lab when she was an undergraduate student five years ago when I just recently joined UNAM as a researcher fresh out of a postdoc stay. After getting her B.Sc. degree and publishing an article in JCTC (DOI: 10.1021/ct4004178) she now is about to publish more papers that I’m sure will be as highly ranked as the previous one. Thus, Maru was a pioneer in our lab giving it a vote of confidence when we had little to nothing to show for; thanks to her hard work and confidence, along with that of the students who have followed her, we managed to succeed as a consolidated research group in the field of computational chemistry.
More specifically, her thesis centered around finding a mechanism for the excitonic transference between pigments (bacteriochlorophyl-a, BChl-a) in the Fenna-Matthews-Olson (FMO) complex, a protein trimer with seven BChl-a molecules in each monomer, located between the antenna complex and the reaction center in green sulfur bacteria. Among the possible mechanisms explored were Förster’s theory, a modification to Marcus’ theory and finally we explored the possibility of Singlet Fission occurring between adjacent molecules with the help of Dr. David Casanova from the Basque Country University where Maru took a short research stay last autumn. Since nature doesn’t conform to any specific mechanism -specially in a complex arrangement such as the FMO- then it could be possible that a combination of the above might also occur but lets just wait for the papers to be published to discuss it. Calculations were performed through the TD-DFT and the C-DFT formalisms using G09 and Q-Chem; comparing experimental data in CH3OH (SMD implicit calculations with the SVWN5 functional) were undertaken previously for selection of the level of theory.
Now, after two original theses written and successfully defended, an article published in JCTC and more in process, at least five posters, a couple of oral presentations and countless hours at her desk, Maru will go pursuit a PhD abroad where I’m sure she will exceed anyone’s expectations with her work, drive, dedication and scientific curiosity. Thank you, Maru, for all your hard work and trust when this lab needed it the most, we wish you the best for you earn it. You will surely be missed.
I don’t know why I haven’t written about the Local Bond Order (LBO) before! And a few days ago when I thought about it my immediate reaction was to shy away from it since it would constitute a blatant self-promotion attempt; but hell! this is my blog! A place I’ve created for my blatant self-promotion! So without further ado, I hereby present to you one of my own original contributions to Theoretical Chemistry.
During the course of my graduate years I grew interested in weakly bonded inorganic systems, namely those with secondary interactions in bidentate ligands such as xanthates, dithiocarboxylates, dithiocarbamates and so on. Description of the resulting geometries around the central metallic atom involved the invocation of secondary interactions defined purely by geometrical parameters (Alcock, 1972) in which these were defined as present if the interatomic distance was longer than the sum of their covalent radii and yet smaller than the sum of their van der Waals radii. This definition is subject to a lot of constrictions such as the accuracy of the measurement, which in turn is related to the quality of the monocrystal used in the X-ray difraction experiment; the used definition of covalent radii (Pauling, Bondi, etc.); and most importantly, it doesn’t shed light on the roles of crystal packing, intermolecular contacts, and the energetics of the interaction.
This is why in 2004 we developed a simple yet useful definition of bond order which could account for a single molecule in vacuo the strength and relevance of the secondary interaction, relative to the well defined covalent bonds.
Barroso-Flores, J. et al. Journal of Organometallic Chemistry 689 (2004) 2096–2102 http://dx.doi.org/10.1016/j.jorganchem.2004.03.035,
Let a Molecular Orbital be defined as a wavefunction ψi which in turn may be constructed by a linear combination of Atomic Orbitals (or atom centered basis set functions) φj
We define ζLBO in the following way, where we explicitly take into account a doubly occupied orbital (hence the multiplication by 2) and therefore we are assuming a closed shell configuration in the Restricted formalism.
The summation is carried over all the orbitals which belong to atom A1 and those of atom A2.
Simplifying we yield,
where Sjk is the overlap integral for the φj and φk functions.
By summing over all i MOs we have accomplished with this definition to project all the MO’s onto the space of those functions centered on atoms A1 and A2. This definition is purely quantum mechanical in nature and is independent from any geometric requirement of such interacting atoms (i.e. interatomic distance) thus can be used as a complement to the internuclear distance argument to assess the interaction between them. This definition also results very simple and easy to calculate for all you need are the coefficients to the LCAO expansion and the respective overlap integrals.
Unfortunately, the Local Bond Order hasn’t found much echo, partly due to the fact that it is hidden in a missapropriate journal. I hope someone finds it interesting and useful; if so, don’t forget to cite it appropriately 😉
Calculating both Polarizability and the Hyperpolarizability in Gaussian is actually very easy and straightforward. However, interpreting the results requires a deeper understanding of the underlying physics of such phenomena. Herein I will try to describe the most common procedures for calculating both quantities in Gaussian09 and the way to interpret the results; if possible I will also try to address some of the most usual problems associated with their calculation.
The dipole moment of a molecule changes when is placed under a static electric field, and this change can be calculated as
pe = pe,0 + α:E + (1/2) β:EE + … (1)
where pe,0 is the dipole moment in the absence of an electric field; α is a second rank tensor called the polarizability tensor and β is the first in an infinite series of dipole hiperpolarizabilities. The molecular potential energy changes as well with the influence of an external field in the following way
U = U0 – pe.E – (1/2) α:EE – (1/6) β:EEE – … (2)
Route Section Keyword: Polar
This keyword requests calculation of the polarizability and, if available, hyperpolarizability for the molecule under study. This keyword is both available for DFT and HF methods. Hyperpolarizabilities are NOT available for methods that lack analytic derivatives, for example CCSD(T), QCISD, MP4 and other post Hartree-Fock methods.
Frequency dependent polarizabilities may be calculated by including CPHF=RdFreq in the route section and then specifying the frequency (expressed in Hartrees!!!) to which the calculation should be performed, after the molecule specification preceded by a blank line. Example:
#HF/6-31G(d) Polar CPHF=RdFreq Title Section Charge Multiplicity Molecular coordinates ==blank line== 0.15
In this example 0.15 is the frequency in Hartrees to which the calculation is to be performed. By default the output file will also include the static calculation, that is, ω = 0.0. Below you can find an example of the output when the CPHF=RdFreq is employed (taken from Gaussian’s website) Notice that the second section is performed at ω = 0.1 Ha
SCF Polarizability for W= 0.000000: 1 2 3 1 0.482729D+01 2 0.000000D+00 0.112001D+02 3 0.000000D+00 0.000000D+00 0.165696D+02 Isotropic polarizability for W= 0.000000 10.87 Bohr**3. SCF Polarizability for W= 0.100000: 1 2 3 1 0.491893D+01 2 0.000000D+00 0.115663D+02 3 0.000000D+00 0.000000D+00 0.171826D+02 Isotropic polarizability for W= 0.100000 11.22 Bohr**3.
You may have noticed now that the polarizabilities are expressed in volume units (Bohr^3) and the reason is the following:
Consider the simplest case of an atom with nuclear charge Q, radius r, and subjected to an electric field, E, which creates a force QE, and displaces the nucleus by a distance d. According to Gauss’ law this latter force is given by:
(dQ^2)/(4πεr^3) = QE (Hey! WordPress! I could really use an equation editor in here!)
if the polarizability is defined by Qd/E then we can rearrange the previous equation and yield
α = 4πεr^3 which in atomic units yields volume units, r^3, since 4πε = 1. This is why polarizabilities are usually referred to as ‘polarizability volumes’.
****THIS POST IS STILL IN PROGRESS. WILL COMPLETE IT IN SHORT. SORRY FOR ANY INCONVENIENCE****
The use of double zeta quality basis sets is paramount but it also makes these calculations more time consuming. Polarization functions on the basis set functions are a requirement for good results.
As usual, please rate/comment/share this post if you found it useful or if you think someone else might find it useful. Thanks for reading!
Is the C atom in methane sp3 hybridized because it’s tetrahedral or is it tetrahedral because it’s sp3 hybridized? It’s funny how many students think to this date that the correct answer is the latter; specially those working in inorganic chemistry. I ignore the reason for such trend. What is true is that most chemistry teachers seem to have lost links to certain historical facts that have shaped our scientific discipline; most of those lay in the realm of physics, maybe that’s why.
What Linus Pauling, in a very clever way, stated was that once you have a set of eigenvectors (orbitals) of the atomic Hamiltonian any combination of them will also be an eigenvector (which is normal since one of the properties of Hermitian operators is that they are linear); so why not making a symmetry adapted one? Let’s take the valence hydrogenoid orbitals (hydrogenoid being the keyword here) and construct a linear combination of them, in such a way that the new set transforms under the irreducible representations of a given point group. In the case of methane, the 2s and 2p orbitals comprise the valence set and their symmetry-adapted-linear-combination under the Td point group constitutes a set of new orbitals which now point into the vertexes of a tetrahedron. Funny things arise when we move to the next period of the table; it has been a controversy for a number of years the involvement of empty d orbitals in pentacoordinated P(V) compounds. Some claim that they lay too high in energy to be used in bond formation; while others claim that their involvement depends on the nature (electronegativity mainly) of the surrounding substituents.
In many peer reviewed papers authors are still making the mistake of actually assigning a type of hybridization to set of valence orbitals of an atom based on the bond angles around it. Furthermore, it is not uncommon to find claims of intermediate hybridizations when such angles have values in between those corresponding to the ideal polyhedron. Symmetry is real, orbitals are not; they are just a mathematical representation of the electron density distribution which allows us to construct mind images of a molecule.
Linus Pauling is one of my favourite scientific historical figures. Not only did he build a much needed at the time bridge between physics and chemistry but he also ventured into biochemistry (his model of an alpha-helix for the alanine olygopeptide became the foundation to Watson & Cricks later double helix DNA model), X-ray diffractometry, and humanities (his efforts in reducing/banning the proliferation of nuclear weapons got him the Nobel Peace Prize long after he had already received the Nobel Price in Chemistry). He was a strong believer of ortho-molecular nutrition, suggesting that most illnesses can be related to some sort of malnutrition. Linus Pauling and his book On the Chemical Bond will remain a beacon in our profession for the generations to come.
Disclaimer: The question above, with which I opened this post, was taken from an old lecture by Dr. Raymundo Cea-Olivares at UNAM back in the days when I was an undergraduate student.