In press, available from the SPIE, the International Society For Optical Engineering (don’t ask me). One of the most interesting pieces of information to come from this study, besides discovering the SPIE’s restriction to grey scale images in this day and age, is just how insensitive to basis set the Hirshfeld partitioning method is (across the DN, DND, DNP DMol3 basis sets) and just how sensitive the Mulliken partitioning method is. This is, of course, not new to quantum chemistry, but it is of interest to note that the same basic trends that apply to Gaussian-type basis sets also apply to numerical basis sets (trends, interpretive limitations, what’s the difference?). The plot below shows the relative charges on each symmetry-unique atom in PETN. These trends have significant impacts on the calculation of THz intensities by difference-dipole methods, as is discussed in detail in this article text (I have glossed over quite a bit of analysis and report the charge findings for purely academic reasons).
Damian G. Allis, Darya A. Prokhorova, Anna M. Fedor, and Timothy M. Korter
Abstract: This paper focuses on the establishment of methodologies for the successful application of first principles theoretical analyses in the understanding of the terahertz spectroscopy of molecular solids, particularly high-energy materials. A solid-state density functional theoretical study has been performed on the high explosive pentaerythritol tetranitrate (PETN) in order to address the relationships between the choice of computational parameters and the predictions of molecular and solid-state properties, such as molecular geometries, intermolecular interactions within the crystal cell, charge distributions, and solid-state vibrations in the terahertz (3 to 200 cm-1) region. This investigation has lead to the conclusion that the BP functional has the best overall performance and the choice of basis set is the most critical theoretical variable. Varying other parameters such as grid size, orbital cut-off, and convergence criteria lead to negligible differences among the calculations.
In press, available from the journal Bioconjugate Chemistry. The modeling study for the avidin–biotin structure and the biotin derivatives were completed with the molecular dynamics program NAMD on a Dual G4/450 loaned to me from Apple for development work, for which I am grateful (I’ve performed molecular dynamics simulations with the Walrus). I did manage to smoke the motherboard during this experience, for which I apologize. Given the state of the machine after the autopsy, I’m hoping no one (especially Eric Zelman!) asks for it back, even when I’m 64.
I made mention of the reasons for some of this work in an interview I did for nanotech.biz, completely unrelate to the other content, in case anyone wants some background.
Shelly James, Kevin P. Maresca, Damian G. Allis, John F. Valliant, William Eckelman, John W. Babich, and Jon Zubieta
Abstract: Biotin and avidin form one of the most stable complexes known (KD = 10-15M-1) making this pairing attractive for a variety of biomedical applications including targeted radiotherapy. In this application one of the pair is attached to a targeting molecule while the other is subsequently used to deliver a radionuclide for imaging and/or therapeutic applications. Recently we reported a new single amino acid chelate (SAAC) capable of forming robust complexes with Tc(CO)3 or Re(CO)3 cores. We describe here the application of SAAC analogs for the development of a series of novel radiolabeled biotin derivatives capable of forming robust complexes with both Tc and Re. Compounds were prepared through varying modification of the free carboxylic acid group of biotin. Each 99mTc complex of SAAC-biotin was studied for their ability to bind avidin, susceptibility to biotinidase and specificity for avidin in an in vivo avidin-containing tumor model. The radiochemical stability of the 99mTc(CO)3 complexes was also investigated by challenging each 99mTc-complex with large molar excesses of cysteine and histidine at elevated temperature. All compounds were radiochemically stable for greater than 24 hours at elevated temperature in the presence of histidine and cysteine. Both [99mTc(CO)3(L6)]+1 [TcL6; L6 = biotinyl- amido- propyl- N,N- (dipicolyl)- amine] and [99mTc(CO)3(L12a)]+1 (TcL12; L12 = N,N-(dipicolyl)- biotin- amido- Boc- lysine; TcL12a; L12a = N,N- (dipicolyl)- biotin- amide- lysine) readily bound to avidin whereas [99mTc(CO)3(L9)]+1 [TcL9; L9 = N,N- (dipicolyl)- biotin- amine] demonstrated minimal specific binding. TcL6 and TcL9 were resistant to biotinidase cleavage while TcL12a, which contains a lysine linkage, was rapidly cleaved. The highest uptake in an in vivo avidin tumor model was exhibited by TcL6, followed by TcL9 and TcL12a, respectively. This is likely the result of both intact binding to avidin and resistance to circulating biotinidase. Ligand L6 is the first SAAC analogue of biotin to demonstrate potential as a radiolabeled targeting vector of biotin capable of forming robust radiochemical complexes with both 99mTc and rhenium radionuclides.Computational simulations were performed to assess biotin-derivative accommodation within the binding site of the avidin. These calculations demonstrate that deformation of the surface domain of the binding pocket can occur to accommodate the transition metal-biotin derivatives with negligible changes to the inner-β-barrel, the region most responsible for binding and retaining biotin and its derivatives.
P.S. This publication is also of some use for explaining the series of images on the current departmental brochure for the Syracuse U. Chemistry Department. Steric interactions affect the local geometries of protein binding pockets. And a good thing, too.
Click on the image for a larger version.
That smile. That presence. That fashion sense. Yup, Richard Feynman. First we’re published together in the CRC Handbook of Nanotech, now we find ourselves playing the same second fiddles on the same page to the infinitely more photogenic Giselle Itiê. Not bad, considering he checked out before I entered my teens.
I have no idea what Pablo Nogueira’s article says, but I do know that the folks at Revista Latitude (that’s Latitude Magazine!) spiced the text up with a few primo images available from Rocky Rawstern’s much appreciated nanotech-now.com gallery. Revista Latitude and Revista Top are very visual magazines. The now-ness of a Rolling Stone with the imagery of a National Geographic. I didn’t understand a word but I much enjoyed turning the pages. It does a researcher good to see that a magazine can make science work in same binding with photojournals of exotic destinations or fashion on location.
Calfskin bongos, international models, molecular nanotechnology. I think anyone who finished “Surely You Must Be Joking” would conclude that the man would approve.