Constellation Map generated with Starry Night Pro 6.

Those in the vicinity of Manlius, NY are no doubt aware of the presence of Sno-Top (home of the best soft black raspberry in the area, IMHO) and the duck pond at town center(-ish). Those continuing just a tad further along Fayette Street (92, DeWitt-to-Cazenovia direction) also know that the swan population is localized to the higher pond near the Saucy Swan Restaurant (they do make for loquacious patrons). These facts, combined with the oppressive CNY heat of early July, made the choice of Cygnus the Swan obvious for this month’s constellation. Fittingly, Cygnus is an astronomical feast for naked eye, binocular, and telescope observers alike and, as it is half-way between horizon and zenith in early July in the early evening, it is strategically placed for accessibility with all manner of optics.

Cygnus is surrounded by several dangerous Constellations. The animal Constellations Draco, Velpecula, and Lacerta might enjoy freshly killed what the king Cepheus would otherwise enjoy glazed. The massive Constellation Pegasus is a problem in its own right. Trampled by horse is bad enough on the ground, but to have to avoid trampling by a flying one is another matter altogether. Lyra may be the only reminder to Cygnus of its terrestrial past, having been the instrument of choice for one of Cygnus’ human attributions (that man being Orpheus. See below). For those using only their free pair of 1×7 binoculars (that is, your pair of eyes), the cross that makes up the body and elbows of the wings of Cygnus are most obvious. The bright stars Deneb, Sadr, and Gienah (and the nearby Vega in Lyra, the easiest of the stars in this part of the sky to find starting at sunset) are perhaps most obvious, but the rest of the body is pronounced. As the evening progresses (and on reasonably clear nights), the most striking feature of Cygnus is the river of stars and interstellar dust that is our view of the Milky Way (as if Cygnus is flying above it).

As a collection of prominent stars within the body of the Milky Way, you can guess that the Constellation we know as Cygnus has a long and distinguished history. The Greeks (“Give me a Constellation, any Constellation, and I show you that the history of that Constellation is Greek”) have many swans in their mythology, from Zeus (who fathered Gemini and Helen of Troy disguised as a swan, or so the story goes) to Orpheus (turned into a swan upon his death and placed next to his lyre (Lyra) to characters in Ovid’s Metamorphoses. Cygnus is a member of the “Famed 48,” the 48 original Constellations contained within Ptolemy’s Almagest.

Alberio. From wikipedia.org.

At the head of Cygnus is the star Alberio which, upon inspection with even low-magnification optics, resolves into two stars that make up quite possibly the best color contrast in the northern hemisphere (above, from wikipedia). Alberio A (the orange-ish one), is actually itself a true binary, meaning its two stars are gravitationally bound to one another. It is possible, with scopes larger than 20″ and under excellent conditions, to resolve the two stars, Alberio B (the blue-ish one), is a single star that is not gravitationally bound to Alberio A, making this most famous binary an “optical binary,” one where the two stars look very close but only because of our perspective from Earth. If Cygnus is out, this star always makes its way into the eyepiece of the 16″ scope at Darling Hill. Further, for those who like to get their scopes perfectly focused (especially large binoculars), this combination is an excellent test.

M29. From wikipedia.org.

As is the case with all of the Constellations within the band of the Milky Way, Cygnus is host to several binocular and telescope objects. The two pronounced Messier Objects are M29 and M39, both open clusters. M29 (above, from wikipedia) is famous (to me) for being the one Messier Object that does NOT appear in the index of the Peterson Field Guide To Stars And Planets. Believe me, I have tried several times to find it (just assuming the dark conditions kept me from seeing it. It does appear in the Constellation map, though). This object appears within the binocular field of view of Sadr and is small but worth scanning in dark skies. M39 (below, from seds.org) is similarly nondescript, residing between Deneb and the stars of Lacerta.

M39. from seds.org.

Cygnus becomes quite interesting for its wealth of interesting New General Catalogue (NGC) Objects. The four most prominent objects are the North America Nebula (NGC 7000), the Pelican Nebula (IC 5070), the Veil Nebula (NGC 6960, 6962, 6979, 6992, and 6995), and the Crescent Nebula (NGC 6888). The North America (not American) Nebula (below, with the Pelican Nebula to its right, from wikipedia) is a testament to the only mild imagination of the working observational astronomer. Like many nebulae, details can be pulled out of this object with the use of filters. Depending on the conditions, the best way to confirm this structure exists in your scope is, frankly, to move the scope ever so slightly in the field of view of nearby stars and confirm for yourself that some slightly darkened patch of sky is staying put with respect to the background of stars. This approach, combined with averted vision, is definitely my method of choice for finding the locations of objects I may otherwise miss completely (and we’ve all had the experience of NOT seeing something in a scope that another person can even make detail out of). The very low surface brightness of the nebula makes it an at-least binocular object to observe, but it is noteworthy that this entire North America Nebula is reportedly four times the size of the full Moon. The Pelican Nebula (lower right of the image above) looks more like a Teradactyl to me, but there is some similarity in both (in case you do not see it, the pair of eyes are at upper left (with a bright star in each marking the pupils), the beak extends to the left (and is narrower than a typical pelican), and the body extends to some less structured arrangement down to the lower right).

The North America and Pelican Nebulae, photo by Jason Ware. From wikipedia.org.

The Veil Nebula is a collection of nebulae that make for haunting photos. I am very pleased to have a greyscale image of the Eastern Veil provided by our own Stu Forster (below and in the member gallery). This object is very difficult to observe without an OIII filter, but even an 8″ scope will resolve the detail of this nebula with the filter (it is reported that in excellent sky locations, simply holding this filter to one’s eye will make the Veil Nebula stand out). The Veil Nebula has also been the focus of some considerable Hubble imaging time and a web search for these images is definitely worth one’s time.

The Crescent Nebula. Photo by Stu Forster.

Finally, the Crescent Nebula has also been the focus of some astrophotography time by the good Dr. Forster (below (The Crescent, not Dr. Forster)), appearing to me more like a floating brain than a boring crescent. The Nebula is formed by a Wolf-Rayet star, a type of very hot, massive star with a strong stellar wind. This nebula is actually a double-whammy, as the fast-moving stellar wind from this WR star is colliding with the slower stellar wind from this same star when it was a red giant some 400,000 years earlier.

The Crescent Nebula. Photo by Stu Forster.

Clear skies, Damian

The Interesting Result

The conclusion from the previous study was that the insulin B Chain (figure below) acts as a tether to separate the structured region of insulin (the region with the largest inflexible steric bulk, see below) from the region of the transcobalamin II (TCII) that bind vitamin B12. It was then determined that the approach employed for the B12-insulin bioconjugate, simply linking one biomolecule onto another with known binding and transport properties (this is a common theme in all bioconjugate design), worked because the last 10 residues in the insulin B Chain (B22 to B30) are flexible in solution (they, in fact, cover the insulin binding region in the crystal form, then uncover this region in the biologically active form).

As a general procedure for B12 bioconjugate design, one of the key requirements for a functional product is a tether length that provides sufficient separation between B12 and any molecular structure large enough to affect B12 binding within its transport proteins (makes sense, as a tethered structure that does not enable B12 binding in its transport proteins will find the B12 bioconjugate delivered to the gut where acids and digestive enzymes will hide the failed binding). This leads to the question, “How long must a tether be to meet this rather general criterion?” This is, partly, the correct question, as the retention of B12 binding within its transport proteins is a function of both proper tether length and [transport protein]-["other molecule"] interaction (in this first case, “other molecule” = insulin).

Saving the exhaustive analysis for the paper, this new study used this flexible region of human insulin (that is, B22 to B30, with the B12 linkage occurring on the B29 lysine side chain) as a proxy for any arbitrary tether, then used MD simulations to consider how the flexibility of this tether might lead to changes in B12 binding within its TCII pocket (the transport protein for which we have the best crystal structure). The result of these simulations was the identification of the side chain of lysine itself being just long enough to separate the B Chain tether region from the TCII protein surface. This does not mean that lysine will always serve as a perfect linkage. This means that, if the tether structure is effectively non-interacting with TCII (so not sterically demanding by itself), the lysine side chain is long enough to span the solvent-accessible hole produced by the encapsulation of B12 in (in this case) TCII.

The result is a design constraint when using lysine that is quite fortuitous! If the target peptide (insulin or whatnot) has a surface-accessible lysine side chain within a region that is flexible in solution, some simple amide chemistry may produce a viable B12 bioconjugate for delivering that peptide orally (thereby avoiding complete peptide degradation in the G.I. tract).

The More Interesting Result

Buried deep within the bottom of the Discussion section. If you watch the dynamics simulation of the TCII-[B12-tether] complex (shown below for a 300 K 50 ns simulation with 1.5 fs time steps in 14,000 waters (not shown)), you see that the binding of B12 within TCII and the geometry of the encapsulation complex are strongly linked. That is, TCII (and, presumably, its cohorts in the B12 transport pathway) can be thought of as two quite rigid fragments (Red and Blue in the animation) connected by a long tether (Green) that are separated in solution but brought into contact by the binding of vitamin B12 (Gold). The B12 is a glue that holds the fragments together, and a simple tabulation of hydrogen-bonding interactions in the crystal structure reveal that the B12 has more interactions to the A and B fragments of TCII individually than A and B have with each other (which is to say, the B12-A Segment interaction and B12-B Segment interaction are stronger than the A-B Segment interaction). From a biological perspective, this should make perfect sense. B12 is a large, extremely important biomolecule that, since we do not make it ourselves, is to be captured and transported as effectively as possible. The best way to bind this molecule is not to wait for it to burrow into a binding pocket, but rather to encapsulate it in a “clam shell” maneuver that provides “maximum embedding.” The tether between the A and B Segments technically would not have to be present if the A and B fragments were present in large quantities (although, as you might expect, the A-B tether does considerably reduce the time to complete encapsulation by forcing these fragments within close proximity).

According to the crystal structure, the B12 is entirely embedded within TCII, with only the solvent-accessible hole at the 5′-ribose position readily accessible for bioconjugate formation. If the overall structure were as rigid as a crystal structure might lead one to believe, functionalization at the cobalt position in the corrin ring would be out of the question.

As I just stated that such a binding mode would otherwise be unlikely, you can guess that there are B12 bioconjugates linked at the cobalt ring that are bio-active.

If you watch the dynamics simulation of the TCII-[B12-tether] complex, you see that the clam shell binding mode of TCII is one with a “loose hinge.” This loose hinge is really a result of the flexibility of the two protein fragments (typical protein motion) and flexibility in the short propionamide side chains of vitamin B12 that provide a bit of “spring” in the complete complex. In effect, the flexibility within the structure provides a means for cobalt to be coordinated to something without loss of B12 binding provided that the tether linking the cobalt and the “other” molecule is small enough that it does not require a large change in the A-B binding arrangement (that is, does not affect B12-A and B12-B binding).

And Then There Were Three…

The expectation/prediction/untested hypothesis is that vitamin B12 may be able to happily accommodate two additional molecules at the 5’-ribose and cobalt positions (properly designed) that then provide for the transport of two molecules and/or the delivery of three molecules (one being vitamin B12). This opens the door to a wealth of possibilities, from trinary delivery to combined drug delivery + radiopharma characterization. This is the possibility I’m most interested in pursuing in the next rounds of calculations, with the theory (presumably) providing a very good initial guess about the ideal tether designs to use with B12 for enabling delivery and bio-activity.

And Now For The Hard Work

Stepping back from the theoretical analysis for a moment, the most difficult obstacles to overcome in this study were the generation AND incorporation of force field parameters for vitamin B12 and a B12-Lysine mini-bioconjugate into GROMACS, a problem that I’ve addressed only in passing in several previous posts. What I won’t do in this post is explain the procedure (a single blog post will not do the procedure justice given the complexity of force field parameter generation). What I will do is provide the files for the topology for these systems and a short list of the modifications one needs to make in order to get these systems working. For additional reference, the same topology files are provided in the Supplemental Material for the paper (so, if you find yourself using these, obviously cite the paper and not my humble blog).

Files And Contents:

These are not files to be placed in a single directory, but are segments of file that are going to be placed directly into pre-existing topology files. This is not the best way to do it but is the procedure I began with and will not be changing without finding a very simple tutorial on how-to (which, if you have, I’d be happy to read).

The contents of the topology file (which I assume for you will be ffG53a6 but should work generally) are provided below:

The topology specifications for vitamin B12 (nothing bound to the cobalt in the corrin ring), cyanocobalamin (CN-B12, with a cyanide bound to the cobalt), B12 with a lysine residue attached to the 5’-ribose hydroxyl position (the tether linkage for the GROMACS prep programs), and CN-B12 with a lysine residue attached to the 5’-ribose hydroxyl position.

I am assuming that you’re using the ffG53a6 force field, meaning you add the topology sets to the bottom of the ffG53a6.rtp file.

GROMACS Modifications:

GROMACS force field and topology files must be modified slightly in order to read the topologies generated above and, depending on where you got the B12 structure, add/correct the hydrogen atoms in the B12 molecule.

In a typical UNIX/Linux installation (which I have provided compilation instructions for in a previous post), the files to be modified can be found in /usr/local/gromacs. And, if you’re using Ubuntu like I am, you’ll need to “sudo” these modifications.

1. aminoacids.dat

If you open this file, you see a list of three- and four-letter codes in the format:

50
ABU
ACE
...
VAL
PGLU

The “50” refers to the number of codes. As we’re going to be adding the codes B12, BCN, LYB, and LCB into GROMACS, we first change 50 to 54, then just list the four codes at the bottom of the file:

54
ABU
ACE
...
VAL
PGLU
B12
BCN
LYB
LCB

You’ll note that B12 and BCN aren’t like the others, LYB is not LYS, and LCB is also nowhere to be seen. The codes in this file are STANDARD and make sure you don’t inadvertently name your inserted structure one of the structures in the list.

2. ffG53a6.hdb

I specifically used the ffG53a6 force field for the TCII-B12 work, meaning I only made modifications to these force field files. The ffG53a6.hdb file is responsible for adding/correcting hydrogen atoms in your structure (just because the crystallographers do not see them does not mean they aren’t there) and contains hydrogen-beautification information for all of the three/four-letter codes recognized in aminoacids.dat. The content below is the hydrogen-correcting data for the B12, BCN, LYB, and LCB structures. Simply paste this into the bottom of the ffG53a6.hdb file.

B12     19
1    2    HAO    N62    C61    O63
1    2    HAN    N62    C61    C60
1    2    HAM    N52    C50    O51
1    2    HAL    N52    C50    C49
1    2    HAK    N45    C43    O44
1    2    HAJ    N45    C43    C42
1    2    HAI    N40    C38    O39
1    2    HAH    N40    C38    C37
1    2    HAE    N29    C27    O28
1    2    HAD    N29    C27    C26
1    2    HAG    N33    C32    O34
1    2    HAF    N33    C32    C31
1    2    HAA    O7R    C2R    C1R
1    2    HAB    O8R    C5R    C4R
1    2    HAC    N59    C57    O58
1    1    H2B    C2B    N1B    N3B
1    1    H4B    C4B    C5B    C9B
1    1    H7B    C7B    C8B    C6B
1    1    H10    C10    C9     C11
LYB     20
1    1    H      N      -C     CA
1    4    HZ1    NZ     CE     CD
1    2    HAO    N62    C61    O63
1    2    HAN    N62    C61    C60
1    2    HAM    N52    C50    O51
1    2    HAL    N52    C50    C49
1    2    HAK    N45    C43    O44
1    2    HAJ    N45    C43    C42
1    2    HAI    N40    C38    O39
1    2    HAH    N40    C38    C37
1    2    HAE    N29    C27    O28
1    2    HAD    N29    C27    C26
1    2    HAG    N33    C32    O34
1    2    HAF    N33    C32    C31
1    2    HAA    O7R    C2R    C1R
1    2    HAC    N59    C57    O58
1    1    H2B    C2B    N1B    N3B
1    1    H4B    C4B    C5B    C9B
1    1    H7B    C7B    C8B    C6B
1    1    H10    C10    C9     C11
BCN     19
1    2    HAO    N62    C61    O63
1    2    HAN    N62    C61    C60
1    2    HAM    N52    C50    O51
1    2    HAL    N52    C50    C49
1    2    HAK    N45    C43    O44
1    2    HAJ    N45    C43    C42
1    2    HAI    N40    C38    O39
1    2    HAH    N40    C38    C37
1    2    HAE    N29    C27    O28
1    2    HAD    N29    C27    C26
1    2    HAG    N33    C32    O34
1    2    HAF    N33    C32    C31
1    2    HAA    O7R    C2R    C1R
1    2    HAB    O8R    C5R    C4R
1    2    HAC    N59    C57    O58
1    1    H2B    C2B    N1B    N3B
1    1    H4B    C4B    C5B    C9B
1    1    H7B    C7B    C8B    C6B
1    1    H10    C10    C9     C11
LCB     20
1    1    H      N      -C     CA
1    4    HZ1    NZ     CE     CD
1    2    HAO    N62    C61    O63
1    2    HAN    N62    C61    C60
1    2    HAM    N52    C50    O51
1    2    HAL    N52    C50    C49
1    2    HAK    N45    C43    O44
1    2    HAJ    N45    C43    C42
1    2    HAI    N40    C38    O39
1    2    HAH    N40    C38    C37
1    2    HAE    N29    C27    O28
1    2    HAD    N29    C27    C26
1    2    HAG    N33    C32    O34
1    2    HAF    N33    C32    C31
1    2    HAA    O7R    C2R    C1R
1    2    HAC    N59    C57    O58
1    1    H2B    C2B    N1B    N3B
1    1    H4B    C4B    C5B    C9B
1    1    H7B    C7B    C8B    C6B
1    1    H10    C10    C9     C11

As brief explanation, the three-letter code is followed by the number of Hydrogen atoms that are to be added. Each line can be read:

First Column – The number of hydrogen atoms added (so all of these entries on the far left mean “add ONE hydrogen”)

Second Column – The manner by which the hydrogen atom is to be added (this is listed in section 5.5 of the GROMACS 3.3 Manual (page 93))

Third Column – The name of the Hydrogen atom to be added

Fourth Column – The atom to which the H is going to be directly linked in the topology file

Fifth – Seventh Columns – atoms that define how the Hydrogen is added with respect to (1) the code in Column 2 and (2) the atom to which the Hydrogen is added.

3. ffG53a6bon.itp

There are a few subtle tweaks to the force constants for a few bonds that I perform here right within the file and that proper MD people likely would scream at. I note that, when you do this, you are making changes to numbers that will affect the results if you somehow start doing heme MD simulations.

Change the gb_NN values to those provided below.

#define gb_34        0.198  0.6400e+06
; NR  -   FE    120
#define gb_4         0.1142  3.7000e+07
; C - O (CO in heme)  2220
#define gb_14       0.1340  1.1000e+07
; C  -  NR (heme)       1000
#define gb_30       0.1880  2.7200e+06
; FE  -  C (Heme)

You will note that I have not done anything to make cobalt appear in the topology or force field files. For the sake of running a simulation, Fe and Co are close enough that simply replacing CO for FE in the PDB file is sufficient. You can do the completely proper job of adding cobalt to the force field to get the mass right.

And that is the bare basics for getting a run to happen. A proper tutorial on how to generate force field parameters and topologies may be forthcoming, depending largely on interest and my ability to find time to do it.

Article citation: Damian G. Allis, Mol. BioSyst., 2010, DOI: 10.1039/c003476b

Damian G. Allis¹, Timothy J. Fairchild² and Robert P. Doyle¹

1. Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
2. School of Chiropractic and Sports Science, Murdoch University, Murdoch, WA 6150, Australia

As part of ongoing research into the use of vitamin B12 (B12; cobalamin; Cbl)-based bioconjugate approaches for the oral delivery of peptides/proteins, a molecular dynamics (MD) study of the binding of a cyanocobalamin–insulin (CN–Cbl–insulin) conjugate to human transcobalamin(II) (TCII) was recently reported that provides a qualitative picture of how the human insulin protein in its open T-state geometry affects CN–Cbl binding to TCII. This initial analysis revealed that the B22–B30 segment of the insulin B-chain acts as a long tether that connects the larger combined insulin A/B region to CN–Cbl when this conjugation is performed at the CN–Cbl ribose 5-hydroxy position. The experimental support for this model of the binding interaction is provided by the consequences of the successful delivery of the CN–Cbl–insulin conjugate in the production of significantly decreased blood glucose levels in diabetic STZ-rat models. In efforts to provide a more detailed description of the (CN–Cbl)–TCII complex for modeling Cbl-based bioconjugate designs, the (CN–Cbl)–TCII system and a CN–Cbl conjugate incorporating a flexible tether composed of only the B22–B30 segment of human insulin have been examined by MD simulations. The implications of these simulations are discussed in terms of successful conjugate positioning on Cbl, especially when such sites are not apparent from the diffraction studies alone, and the possibilities, as yet not reported, for dual-tethered Cbl bioconjugates for multi-component drug delivery applications.

Image taken: Nov. 13, 2009

Location: Vesper, NY, USA

Details: The ISS made an early evening fly-by during the last official Public Viewing session for 2009 of the Syracuse Astronomical Society in Vesper, NY. The 6:36 p.m. EST fly-by made it as far as Alcor and Mizar before passing into Earth’s shadow (the Big Dipper is just entering the tree line to our North). Details: Canon SD780 IS, 15″ exposure, 400 ISO.

The original post can be found at spaceweather.com/submissions/…Damian-Allis-ISS_BigDipper_1258219906.jpg. A PDF’ed version of the page from the spaceweather.com site is stored locally for posterity HERE.

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.

The solution, it should be obvious after, is simply to not include the geometry optimization section in the input file. What would otherwise be the following (with arbitrary geometry optimization-like info between [COORDINATES] and [BASIS SETS]…

[COORDINATES]
OPTGEOM
TOLDEG
0.000005
TOLDEX
0.000020
END
END
[BASIS SETS]

becomes…

[COORDINATES]
[BASIS SETS]

One problem solved by simply not having any optimization parameters (again, makes sense and is now google-able).

2. Proper GRIMME Input Format For Long-Range Dispersion Contributions In Crystal09

This is another example where one’s first efforts in translating the manual into calculations may lead to considerable confusion until the proper format is finally identified (by which time you’ve run many pruned-down input tests).

GRIMME
1.05 20. 25.
1.05 20. 25. s6 (scaling factor) d (steepness) Rcut (cutoff radius)
5
1  0.14 1.001 Hydrogen Conventional Atomic number , C6 , Rvdw
6  1.75 1.452 Carbon Conventional Atomic number , C6 , Rvdw
7  1.23 1.397 Nitrogen Conventional Atomic number , C6 , Rvdw
8  0.70 1.342 Oxygen Conventional Atomic number , C6 , Rvdw
17 5.07 1.639 Chlorine Conventional Atomic number , C6 ,'Rvdw

I’m not even sure where the final ,’Rvdw comes from. Your .out file may terminate with the following error (or something similar)…

rank 7 in job 8  korterquad_51438   caused collective abort of all ranks
  exit status of rank 7: killed by signal 9

And the ERROR.peN file with any content will show the following, clearly pointing to a GRIMME-specific error…

 ERROR **** GRIMME_INPUT **** ELEMENT NOT DEFINED:           1

The problem is the additional content within the manual pages for the GRIMME keyword that require pruning (or, at least, some identifier to show what is and what is not needed). The proper GRIMME section above is properly provided in the INPUT file as…

GRIMME
1.05 20. 25.
5
1  0.14 1.001
6  1.75 1.452
7  1.23 1.397
8  0.70 1.342
17 5.07 1.639

Where (see page 88 of the Crystal09 manual)…

GRIMME <- keyword is called
1.05 20. 25. <- scaling factor, steepness, cutoff distance
5 <- number of elements in the list (not the total number of atoms)
1  0.14 1.001 <- atomic number, dispersion coefficient, van der Waals radius
...

When all is properly run, the bottom of your output file will look something like the following:

 CYC  43 ETOT(AU) -5.784662098123E+03 DETOT  1.18E-11 tst  8.17E-15 PX  6.73E-08

 == SCF ENDED - CONVERGENCE ON ENERGY      E(AU) -5.7846620981229E+03 CYCLES  43

 ENERGY EXPRESSION=HARTREE+FOCK EXCH*0.20000+(BECKE  EXCH)*0.80000+LYP    CORR

 TOTAL ENERGY(DFT)(AU)( 43) -5.7846620981229E+03 DE 1.2E-11 tester 8.2E-15
 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT EDFT        TELAPSE     4705.82 TCPU     4651.41

 *******************************************************************************

 GRIMME DISPERSION ENERGY CORRECTION

 SCALE FACTOR (S6):     1.0500

 GRIMME DISPERSION ENERGY (AU) -1.9723347118951E-01
 TOTAL ENERGY + DISP (AU) -5.7848593315941E+03

 *******************************************************************************

The Crystal09 manual refers you to Table 1 of the Stefan Grimme paper, “Semiempirical GGA-type density functional constructed with a long-range dispersion correction” (Journal of Computational Chemistry, Volume 27, Issue 15, Pages 1787 – 1799), which I’ve put together into the proper format below. Be sure to (1) delete the elements in parentheses ( -> get rid of the (H) <- ), (2) remove those atoms you do not need, (3) be sure to change the “number of elements” number for your structure, and (4) get and reference the Grimme paper so you have the proper C6 parameters and van der Waals radii accounted for (you’ll be the right nitwit if I mis-copied something and you ran with it (although I trust my input), and you should have the reference regardless).

( H)   1   0.14 1.001
(Li)   3   1.61 0.825
(Na)  11   5.71 1.144
( K)  19  10.80 1.485
(Rb)  37  24.67 1.628

(Be)   4   1.61 1.408
(Mg)  12   5.71 1.364
(Ca)  20  10.80 1.474
(Sr)  38  24.67 1.606

( B)   5   3.13 1.485
(Al)  13  10.79 1.639
(Ga)  31  16.99 1.650
(In)  49  37.32 1.672

( C)   6   1.75 1.452
(Si)  14   9.23 1.716
(Ge)  32  17.10 1.727
(Sn)  50  38.71 1.804

( N)   7   1.23 1.397
( P)  15   7.84 1.705
(As)  33  16.37 1.760
(Sb)  51  38.44 1.881

( O)   8   0.70 1.342
( S)  16   5.57 1.683
(Se)  34  12.64 1.771
(Te)  52  31.74 1.892

( F)   9   0.75 1.287
(Cl)  17   5.07 1.639
(Br)  35  12.47 1.749
( I)  53  31.50 1.892

(He)   2   0.08 1.012
(Ne)  10   0.63 1.243
(Ar)  18   4.61 1.595
(Kr)  36  12.01 1.727
(Xe)  54  29.99 1.881
Y-Cd      24.67 1.639
Sc-Zn     10.80 1.562

Note that the d-block is identical for each row (so no atom numbers provided).

3. Removing The MPICH2 Content From The Output File In Pcrystal(/09)

This final issue does not occur in Pcrystal(/06) but does in Pcrystal(/09), with the reason being (I assume) the new use of MPICH2 in Pcrystal(/09) instead of MPICH in Pcrystal(/06).  The problem comes from running the following set of commands at the terminal window in MPICH2:

mpiexec -machinefile machine -np N /path/to/Pcrystal &>FILENAME.out &

Embedded within the FILENAME.out file will be all flavors of MPI-specific output, perhaps such as the following (in this case errors, but it happens in proper output as well):

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
rank 7 in job 9  korterquad_51438   caused collective abort of all ranks
 exit status of rank 7: return code 1
rank 4 in job 9  korterquad_51438   caused collective abort of all ranks
 exit status of rank 4: killed by signal 9

or…

mpiexec_machine (handle_stdin_input 1089): stdin problem; if pgm is run in background...
mpiexec_machine (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &

The solution is to break up the mpiexec output from the Pcrystal output, performed by directing the mpiexec-specific content to, in this case, /dev/null (because it is not necessary except for diagnostic purposes).

mpiexec -machinefile machine -np N /path/to/Pcrystal < /dev/null &>FILENAME.out &

Which removes all traces of mpi-specific output from FILENAME.out.

Constellation Map generated with Starry Night Pro 6.

It is only fitting that, as we approach Summer and the unbelievable wealth of binocular and telescope objects that reside within the central region of the Milky Way, we spend at least one article on an otherwise mundane (to the amateur astronomer, anyway) Constellation. We endeavor this act of balance in the presentation of night sky viewing (and in the interest of accounting for all of the sky by the time these articles are done) by featuring Libra, The Scales.

The history of Libra in Western culture is one of science, religion, theft, imminent domain, here-say, and whatever existed as copyright in the Roman days (it is tough to make a Constellation associated with the Law interesting enough for prime time TV, as the only thing there is to murder is the presentation of any historical interpretation attributed to it). The reference to this collection of stars as a balance is reported to go as far back as the Sumerians (approximately 2000 B.C.), where this collection was known as “ZIBBA AN-NA”, or the “balance of heaven.” It is of particularly humorous irony this month that the Greeks were responsible for the disappearance of “the balance” from the night sky in favor of over-inflating the magnitude of the already important constellation Scorpius (for historical perspective, this article is being written as Greek economic infrastructure is falling apart faster than the Parthenon during the Siege of Athens in 1687 by Francesco Morosini, the Doge of Venice [as a good Greek, I shake my fist at the Gods in anger]).

The Romans saw fit to either return to the Sumerian tradition or simply declaw Scorpius, as Libra once again became a set of Scales. It is fate that the pinchers of an arthropod would be returned to the type of covering for reptiles. With the first publications of Libra-friendly star groupings and names upon the demotion of the now more diminutive Scorpius, one might even argue that the pen is mightier than the claws.

When not being visually accosted by rock n’ roll advertisements for lawyers behind cheap bookcase backdrops offering beaucoup bucks for your injury settlements, the legal profession often seems quite dull and arcane in its own right (sorry, Ray). Libra is equally subdued in its presentation, offering no Messier Objects within its official borders and no other really “interesting” things observable through binoculars or small telescopes. Perhaps the most interesting aspect about the constellation itself is its identification as the only inanimate object of the Zodiac, the ring of Constellations that encompass the ecliptic, or the apparent path of the Sun throughout the year.

That is not, however, to say that there isn’t anything worth its weight in hydrogen residing within the Libra boundaries. If we perform a considerable zooming in just above Zubeneschamali (phew! That translates to the “northern claw,” just as its counterpart Zubenelgenubi translates to the “southern claw.” These names would indicate that Arab astronomers opted to use both Greek and Roman sources despite the obvious conflict in the star groupings), we can see (with very good scopes) the star Gliese 581 (shown below), home of one of the most populated planetary systems yet discovered (although it is important to remember that this number is only of those planets we can detect, which means those with significant gravitational influence on their stellar anchor). This is marked “1” in the opening image. To date, there are four detected stars around Gliese 581 (note that the star name is always first, followed by a letter designation), including Gliese 581 b, a Neptune-sized object with a 5.4 day orbit, c, a rocky Earth-like planet within the Gliese 581 Habitable Zone 1.5 times wider and 5 times more dense than our own, d, a planet 1/2 as massive as Uranus and still within in the Habitable Zone, and e, a planet 1.6 times as massive as Earth and the smallest yet identified. the star Gliese 581 not only represents a feat of mathematical prowess on the part of Terran researchers, but is also of specific interest because of the number of planets within its Habitable Zone, the region within which conditions are believed to be similar to our own (specifically, liquid water on the surface). Some even refer to this as the “Goldilocks Zone,” where it’s not too cold and not too hot. One might say that this region is where a proper balance of hot and cold is reached…

Gliese 581

Of all of the asterisms (groups of stars that are not designated as Constellations but that still have specific meaning. For instance, the Big Dipper is an asterism within the Constellation Ursa Major) that have jumped out at me during my binocular viewing adventures, the one marked by the “2″ is perhaps the one that most stood out to my eyes. It is one of the most perfect isosceles triangles in the nighttime sky and is reasonably clear around it such that only this shape stands out in low-power optics. When it’s out, I always look for this small golden nugget residing within the Zubeneschamali-side of the scales, tipping the balance towards the arrival of the Summer constellations Scorpius and Sagittarius, the pair that mark the inside of our own galaxy and where a disproportionate number of Messier riches abound.

Constellation Map generated with Starry Night Pro 6.

I continue to groom the Eastern sky in this month’s Constellation presentation by spending some time conditioning you to appreciate the subtle shapeliness and glowing highlights just a short clip from last month’s subject, Canes Venatici (I will endeavor to refrain from additional dry hair humor in the rest of the article). Coma Berenices, or “Berenice’s Hair,” is an unusual constellation in many respects. It is one of the few constellations that owes its name (and history) to an actual person, is one of the constellations that was promoted from a lowly asterism, it marks the location of the North Galactic Pole, and, as one of the edge-sharing constellations with Virgo, Coma Berenices contains a plethora of Messier Objects (and is an excellent constellation to have memorized if binocular viewing is in your future and you just don’t wanna wait to find something). As has been a general theme with many of these past articles, even the most simple constellations have weaved into them a wealth of astronomical treasures.

“The lives of the priests were almost cut as short as Queen Berenice’s hair.” I have to assume this line has been told in one form or another over the course of the last few millennia as part of the discussion of this simple right angle. Queen Berenice II was the wife of King Ptolemy III Euergetes of Egypt, perhaps best known as the monarch under whom the great port city of Alexandria, home to such notable Greek mathematicians as Euclid and Pappus (you did know what I meant by a “right angle,” didn’t you?) rose to prominence. As history tells us, Ptolemy rode off to seek revenge for the death of his sister, Berenice promised the goddess Aphrodite her hair upon Ptolemy’s safe return, Aphrodite saw fit to collect on said offering, and Berenice offered her golden locks to Afro, er, pardon, Aphrodite’s temple. As if her bad hair day were not enough, the next morning found her offering gone from the temple. The court astronomer Conon of Samos offered the most logical explanation (much to the relief of the temple priests, who were close to getting a far-too-close shave of their own), one which was so convincing that it remains with us today. Aphrodite, well, washed that hair right away from those men, and sent it on its way… skyward. What we now know as Coma Berenices had, at one time (and likely for some amount of time after), been the furry end of the tail of Leo the Lion, Berenice’s close and equally blonde companion. It is believed that Come Berenices graduated from asterism (simply any collection of stars that are NOT official constellations) to constellation with the help of Tycho Brahe in his 1602 star catalogue (reinforced by Johann Bayer in his 1603 work, Uranometria).

The dwarf planet Makemake.

It is a testament to the changing times that I can mention the presence of a planetary neighbor tangled in Coma Berenices that I would not have known to mention when the new SAS newsletter began its membership cycle only two years ago. The dwarf planet Makemake (shown above from a Hubble image and provided to wikipedia by Mike Brown, its discoverer) is currently veryvery close to the south-most bright star, gamma-Com. While helping to provide a marker for one of the smallest catalogued objects in the Night Sky, Coma Berenices also marks an important location for our most important source of observables in the same Sky. The North Galactic Pole (position shown below), is the point 90 degrees above us with respect to the galactic plane (the discussion of the Galactic Coordinate System is far too, well, large to include here, so I refer you to its wikipedia entry HERE).

The North Galactic Pole

Coma Berenices hosts a single Messier Object that is not a galaxy, although, like hair, detail is based on proximity. M53 is a bino-visible (7.7 magnitude) globular cluster approximately 65,000 light years away. As is often the case, our terran view (especially in CNY) does not do this object the justice provided by our tax dollars in the form of Hubble images (shown below). Looking at the constellation image at the top of this article, you may notice a bit of a knot just to the right of Makemake. As it happens, the density of stars in this region of Coma Berenices is high enough that is does have a designation as the very open cluster Melotte 111 in the less well known “other-M” Melotte catalogue. We are far too close to it for the cluster to appear to us as something like the densely-packed Pleiades, but there may be a close-by planet to the Pleiades saying the same thing about the region around our gamma-Com!

M53

The rest of the Messier Objects in Coma Berenices are galaxies, with all but one of them bright (close-by) members of the Virgo Cluster, the gigantic collection of up-to 2000 galaxies discussed briefly in last month’s newsletter. Coma Berenices and its border with Virgo are regions that all Messier Marathoners cannot wait to have appear prominently in their early-morning March skies, as finding and checking-off these objects in your race-to-the-finish search as fast as two-in-one shampooing. The six Virgo members are (listed top-down) M85, M100, M98, M99, M88, and M91. You will note that M86, M84, M90, M89, M87, M58, M59, and M60 (phew!) are also in very close proximity in Virgo. Your problem is not finding smudge patches in your binoculars. You’re problem is finding out which one you’re looking at!

The lenticular (a morphological hybrid between elliptical and spiral galaxy shapes) galaxy M85 (NGC 4382) marks the northernmost edge of the Virgo cluster. Admittedly, the detail in the Hubble image is a bit lacking (shown below), one of the signs of an old elliptical galaxy where star formation is no longer ongoing in any significant amount). This galaxy lies 60 million light years away and is the 94th MOST distant Messier Object. With M85 centered in your Telrad, you’ll find M100 just at the edge of your outer ring.

M85

M100 (NGC 4321, shown at below-left from ESO) has a shape to it that all likely think of when they picture a galaxy in their mind’s eye. One of the most prominent members of the Virgo cluster, this “grand design spiral” galaxy is 55 million light years away and has been observed intensely enough for us to know that it hosts the satellite galaxy NGC 4323. As galaxies go, M100 is jumpin’ with supernovae, with five catalogued since 1901. Centering your Telrad on M100, M99 approaches your outer ring by about the amount that M98 and M88 sits beyond it.

M100

We see the spiral galaxy M98 (NGC 4192, shown below, from Astrofotografia) almost edge-on, making for a view similar to, but less interesting that, the Andromeda Galaxy (M31). If you’re keeping excellent track of your Doppler shifting, you’ll note that M98 is racing towards us at 125 km/sec which, at 60 million light years away, gives us plenty of time to hit the salon before its arrival.

The image of the pinwheel-looking (a name that already has the galaxy M33 associated with it) M99 (below), was taken by amateur astronomer Hunter Wilson and is currently the choice image at wikipedia for this galaxy (no small feat considering the telescope competition both on the ground AND in orbit). The slight unwinding (well, slight to our eyes, but tens of thousands of light years fit into that gap) of the right-most arm is attributed to VIRGOHI21, a region of hydrogen gas and a massive amount of presumed dark matter.

M99

The spiral galaxy M88 (NGC 4501, shown below and also by Hunter Wilson) is racing towards the center of the Virgo cluster (in the direction of M87). This galaxy is noteworthy for its very tight and very regular spiraling that falls smoothly all the way to the galaxy core, home of a supermassive black hole 80 million times the mass of the Sun.

M88

The last Messier member of the Virgo cluster in Coma Berenices is M91 (NGC 4548, shown below). Messier (in 1781) and Herschel (in 1784) both lay claim to its discovery despite the gap in timing. The linked picture for this image is as noteworthy for the soft blending of nebulosity and starry regions as for the multitude of small galaxies also contained in the field of view. Well worth a look.

M91

Finally, the outlier Messier galaxy in this region is M64 (NGC 4826, shown below), known to amateur astronomers as the Black Eye Galaxy. This view is obvious even in our telescopes! Not only is the galaxy interesting for the dark band pointed towards us, but it has become doubly-interesting recently with the discovery that the black band is spinning in the opposite direction of the rest of the galaxy, with the current hypothesis being that the black band is the remains of a companion galaxy that may have collided with the central galaxy one billion years ago. when you next see it, think of the astronomer Conon and the priests he saved from a similar fate.

M64

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

The cover image is meant to convey as much useful information as possible without any verbiage, although this is clearly not a concept meant to be crystal clear to a non-chemist (but kudos if you got the idea without my having to address it).

Included below are the four iterations involved in the cover draft, between which a considerable amount of verbal back-and-forth occurred (that is discussed briefly) to get what was intended to be presented. The iterations are provided both to show how different visions of what might be seen as the most-key of the key points change as content is presented to the client/researcher and, frankly, these all involved quite a bit of busy work and it seems a shame to not have them floating around somewhere accessible.

The original cover idea (above) was quite mundane but provided a bit more information (cryptic as it may appear to the non-mechanistic organic chemist) about what might be occurring in the absence of a brief read of the introduction of the article. This image emphasizes that a constant rearrangement occurs of the vinylcyclobutane (by the many, many arrows and the four different arrangements of deuteriums in the rearrangement) but does not address that the other 12 structures are products of reactions that are generated as the vinylcyclobutane rearranges and undergoes other but simultaneous intramolecular reactions. The absence of the connection between the rearrangement and the formation of products (which include the vinylcyclobutanes) removed this first iteration from the final running.

The second iteration (above) is a significant (well, I think so) improvement in the getting-across of the business end of the research. The vinylcyclobutane rearrangement is still central to the preferred emphasis of the cover (soon to go away) and the connection between the rearrangement and the formation of products is now hinted at directly by the use of the faded arrows. The second-tier information passed along in this image is that the vinylcyclobutane is one of the products, which is not stressed in the image (by the inclusion of four additional arrows from the central graphic (and, with that addition, the inclusion of arrows feeding the vinylcyclobutanes back into the center). If this had been an Angew. Chemie article, the circular design would have been a perfect fit.

It was at this point that a new piece of content was provided in the form of a medium-resolution digital photo of a piece of artwork by Anne Baldwin. The artwork was chosen as much for the colors as for the chaotic quality of the swirls, which was the one aspect of the entire process that the previous two images did not address and which Dr. Baldwin saw as the more significant point to convey. Some Gaussian blurring and a Gaussian basis set later, the new reactant/product combination as scrambled to complement the background and to make clear that one molecule (that at the arrow) lead to everything else in the image, including itself. The slight red halo around the deuterium (dark blue) is a result of an overlay of the blue spheres and red spheres rendered with slightly larger radii.

The arrow color and shading was stolen from Jean-Michel Folon. Example (The Cry) below. If you’ve one of the copies of La morte di un albero (mine is #630), see Comme un aimant (1971).

I admittedly prefer this (that is, the above cover idea) to the final version as the arrow indicates the forward direction of reactions and adds a hint of symmetry to an otherwise jumbled image.

As for the selected cover image (and final iteration, above), the considerable real estate taken up by the vinylcyclobutane in the previous image is recovered, which highlights the starting molecule differently and has the arrow simply angled into a less-busy space.

The final selection may make more sense in light of the image Baldwin chose to use for the graphical abstract.

A word to the perspective cover artist – This is a point that should be obvious but is often not until it is made obvious by an editor when it is much too late. Your images should be as LARGE as possible. Each of the images above is a 200 MB Photoshop file that would print without pixilation or granularity at 600 dpi on a 24” x 36” poster.

ON THE COVER: Scientists are investigating ways to develop effective oral insulin therapies. One such model is a vitamin B12–insulin conjugate bound to transcobalamin II and is shown here docked in the insulin receptor. The discovery of easier ways to deliver insulin into the blood stream would improve the lives of the millions of individuals living with diabetes. This month’s issue of Clinical Chemistry contains 4 articles related to diabetes. The first 2 articles provide readers with a point/counterpoint discussion of the value of reporting estimated glucose along with Hb A1c. Next is an article on the association of apolipoprotein B with incident type 2 diabetes. Lastly, the development of the first radioimmunoassay for insulin led to a Nobel Prize and is chronicled in this month’s Citation Classic feature. (See pages 545, 547, 666, and 671.) Image reproduced with permission from Damian G. Allis and Robert P. Doyle, Department of Chemistry, Syracuse University.

As a brief explanation of the image, this “scene” is meant to show (without proper molecular dynamics simulations to show how well it would work) that the Transcobalamin(II) transport/protection protein for cobalamin/cyanocobalamin (vitamin B₁₂) and the B₁₂-insulin bioconjugate discussed in the ChemMedChem article is small enough to fit within the Insulin Receptor protein such that insulin may still be able to bind to its receptor. This is the final piece of the puzzle in the proposed mechanism (and experimentally demonstrated event) by which the B₁₂-insulin bioconjugate retains all of the benefits of free B₁₂ (transport from the digestive system to the bloodstream) and insulin (proper receptor binding and the subsequent induction of cellular glucose uptake).

The figure caption and April 2010 Table of Contents can be found in PDF format at the Clinical Chemistry website (with a local copy of the PDF also available HERE.

www.somewhereville.com/?page_id=985
www3.interscience.wiley.com/journal/122250806/issue
www.somewhereville.com/?p=511
www.clinchem.org
en.wikipedia.org/wiki/Diabetes
en.wikipedia.org/wiki/Molecular_dynamics
en.wikipedia.org/wiki/Cyanocobalamin
en.wikipedia.org/wiki/Vitamin_B12
en.wikipedia.org/wiki/Bioconjugate
en.wikipedia.org/wiki/Insulin_receptor
www.clinchem.org/content/vol56/issue4/

Constellation Map generated with Starry Night Pro 6.

It often seems to me that the night is much more alive and richly colored than the day.
Vincent van Gogh to his brother Theo, 1888

If the Hubble Ultra Deep Field image has taught us nothing else, it is that every piece of the sky, regardless of how diminutive it may be in the two-dimensional view of the universe through our eyes, holds a wealth of astronomical treasures.  We begin the 2010 Constellation presentations with one such small, but by no means insignificant, piece of the sky.  Canes Venatici (“Now that’s Italian(-sounding)!”) is a young constellation, one of the many additions formalized by Johannes Hevelius in the 17th century and the result of some rather troublesome bookkeeping over the course of written history.  As the story goes, several of the stars within the modern borders of Canes Venatici were originally part of Boötes‘ staff (or club.  Some herdsmen take the protection aspect of their job very seriously).  A poor translation of Ptolemy‘s Almagest from Greek to Arabic to Latin resulted in the “hook” of the staff being turned into “dogs” (accordingly to the translation history provided at wikipedia, the translation went from “the spearshaft having a hook” in Arabic to “spearshaft having dogs” in Latin.  Perhaps the Arabic-to-Latin translation occurred on a late Friday afternoon before a much-anticipated Public Viewing session?). Befitting a new constellation of hunting dogs now accompanying Boötes in his nighttime watch, Hevelius, er, ran with it and gave the mythological canines Chara and Asterion a small but astronomically busy place next to their master.

The two dogs Chara (represented by the star “Chara”) and Asterion (represented by “Cor Caroli”) are identified by only their two brightest stars, which are themselves joined by a short leash in the modern line representation.  The many dimmer stars in this constellation that jump out even with low-power binoculars add multiple “spots” to the imagined bodies of these two dogs.  As they rush ahead of their master Boötes, they point straight towards the hindmost of Ursa Major (or appear to be running past the Big Dipper).  If celestial real estate is any measure of actual size in the ancient illustrations, the giant Ursa Major is right in aligning his gaze away from the two diminutive playful pups.  I’m sure there’s some imagined connection between Canes Venatici and its final bordering constellation Coma Berenices, but I was once told that the explanation can get a little hairy (if you did not recognize that as a poor pun, do read the wikipedia entry for Coma Berenices, which may find its way to a feature in upcoming newsletters).

If we let lying dogs rest for a moment, we find Chara and Asterion in possession of five Messier Objects, including a phenomenal telescope sight that is otherwise most often found by chasing Ursa Major’s tail.  The distance between M3 and M106 marks the total width of this constellation.  M3 (below) is an 8 billion-year-old globular cluster composed of 500,000 stars that rests roughly 1/3 the width of our galaxy from us (33,900 light years).

M3, from Robert J. Vanderbei.

M106 (below, from NASA/CXC/University of Maryland) is one of those distant (well, 25 million light years) galaxies that NASA astronomers have a field day with as they overlay various wavelengths to make visually stunning images.  The strong X-ray lines in its spectrum indicate that a supermassive black hole resides in this galaxy that is in the process of devouring large swaths of stellar and gaseous matter.

M106, from NASA/CXC/University of Maryland.

M94 (below), also known as the Cat’s Eye Galaxy, is a remarkable structure, as it contains two distinct spiral regions in one galaxy (providing the bright central pupil and the darker edges of the eye).  Speaking of two significant features in one, its discovery is attributed to Pierre Mechain and its cataloging by Charles Messier, occurring just two days later (pairs come in three’s?).  M94 is itself the most prominent member of the so-called M94 Group of Galaxies, a closely associated group of (up-to 24) galaxies within the much larger Virgo Supercluster.  Fourteen of these galaxies lie between 9.0 (M94) and 14.2 magnitude, making the search possible with available gear but only under most ideal viewing conditions.

M94, from Spitzer, GALEX and R. Jay GaBany.

The Sunflower Galaxy (M63, below) was one of the first galaxies to have a distinctive spiral quality associated with it (this by Lord Rosse in the mid-19th century).  The short and tightly spiraled arms pack considerable spectral density into a seemingly small space, providing the stem-free sunflower view that, as it contains tens of thousands of suns, might better be called The Galaxyflower.  M63 is a member of the M51 Group, another cluster of galaxies within the Virgo Supercluster that feature, as their crown jewel…

M63, from NASA and WikiSky.

The Whirlpool Galaxy (M51, below) is, perhaps, the third best view of any galaxy to be found at Darling Hill (the second-best being the Andromeda Galaxy (M31) and the first being, you guessed it, our own Milky Way).  We view the Pinwheel Galaxy looking straight down the rotation axis of the pinwheel, providing us with what can be a very clear view of the spiral structure of the galaxy through our scopes (and providing those with big scopes a very clear view of this structure).  I suspect not a single member with a non-GOTO scope has ever said “It’s over in Canes Venatici.”  Instead, I suspect the standard manner of location involves some instruction stating “Look at the last star in the handle of the Big Dipper and go at a right angle about half the distance of the last two stars in the handle.”  If you can see the famous pair Alcor and Mizar in the Big Dipper, you’re almost at M51 in a pair of binoculars.  The bright bulge at the end of one spiral arm is a true companion galaxy.  Computer models indicate that the distortions of the M51 arm at this companion position are a result of the companion galaxy passing through the plane of the M51 some 550 million years ago, as if M51 were in the process of throwing its companion out into the void to be retrieved by our two dogs.

M51, from NASA and ESA.

Lord Rosse, who also identified the spiral structure in M63, observed and sketched the clear spiral structure of M51 in 1845 (shown below).  The sketch he made reminds me of the center swirl within Vincent Van Gogh’s “Starry Night” (shown below).  And speaking of fine art, the Hubble image of M51 (provided as a massive download here) is one of those views that might well make the final cut in the first intergalactic exhibition.

The proverbial “Cat’s Meow” of nighttime viewing from a small pair of stars that mark a small pair of dogs that were spared from the celestial kennel thanks to a mistranslated description of a cudgel.

Clear skies, Damian

www.syracuse-astro.org
www.starrynight.com
en.wikipedia.org/wiki/Vincent_van_Gogh
en.wikipedia.org/wiki/Hubble_Ultra_Deep_Field
en.wikipedia.org/wiki/Universe
en.wikipedia.org/wiki/Canes_Venatici
en.wikipedia.org/wiki/Johannes_Hevelius
en.wikipedia.org/wiki/Bo%C3%B6tes
en.wikipedia.org/wiki/Ptolemy
en.wikipedia.org/wiki/Almagest
en.wikipedia.org/wiki/Canes_Venatici#History
en.wikipedia.org/wiki/Ursa_Major
en.wikipedia.org/wiki/Coma_Berenices
en.wikipedia.org/wiki/Charles_Messier
en.wikipedia.org/wiki/Messier_3
www.princeton.edu/~rvdb/images/NJP/m3.html
en.wikipedia.org/wiki/Messier_106
en.wikipedia.org/wiki/X-ray
en.wikipedia.org/wiki/Supermassive_black_hole
en.wikipedia.org/wiki/Messier_106
gallery.spitzer.caltech.edu/Imagegallery/image.php?image_name=ssc2007-06a
en.wikipedia.org/wiki/M94
en.wikipedia.org/wiki/Pierre_Mechain
en.wikipedia.org/wiki/M94_Group
en.wikipedia.org/wiki/Virgo_Supercluster
ssc.spitzer.caltech.edu/legacy
galexgi.gsfc.nasa.gov/docs/galex/surveys/NGS.html
www.cosmotography.com/index.html
en.wikipedia.org/wiki/Messier_63
en.wikipedia.org/wiki/Lord_Rosse
en.wikipedia.org/wiki/M51_Group
en.wikipedia.org/wiki/Messier_63
en.wikipedia.org/wiki/NASA
en.wikipedia.org/wiki/WikiSky
en.wikipedia.org/wiki/Whirlpool_Galaxy
en.wikipedia.org/wiki/Andromeda_Galaxy
en.wikipedia.org/wiki/Milky_Way
en.wikipedia.org/wiki/Mizar_%28star%29
en.wikipedia.org/wiki/Whirlpool_Galaxy
en.wikipedia.org/wiki/European_Space_Agency
en.wikipedia.org/wiki/Starry_Night

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