#50, published in ChemMedChem (11 (2016), 9, 1015-1020), DOI:cmdc.201600073.
The key to molecular dynamics simulations is recycling – specifically, going into a first project with enough organization to know how to use everything in the next study. While that first successful connectivity table, parameter assignment, and RESP charge generation for something as Frankenstein-esque as vitamin B12 is the north face of Everest, that next simulation is simply a matter of having atom codes in your PDB file standardized.
And, speaking of PDBs, article #50 has the added bonus of having its own entry in the Protein Databank as 2NA5 – quite a treat (to me, anyway).
And furthermore, this is the first of my publications to benefit from the Research Computing infrastructure on the Syracuse University campus – the throughput of calculations for future work is completely unprecedented in my history of resource access anywhere (the drop in storage prices is very real to some of us).
Authors: Henry K.E., Kerwood D.J., Allis D.G., Workinger J.L., Bonaccorso R.L., Holz G.G., Roth C.L., Zubieta J., and Doyle R.P.
Abstract: Vitamin B12–peptide conjugates have considerable therapeutic potential through improved pharmacokinetic and/or pharmacodynamic properties imparted on the peptide upon covalent attachment to vitamin B12 (B12). There remains a lack of structural studies investigating the effects of B12 conjugation on peptide secondary structure. Determining the solution structure of a B12–peptide conjugate or conjugates and measuring functions of the conjugate(s) at the target peptide receptor may offer considerable insight concerning the future design of fully optimized conjugates. This methodology is especially useful in tandem with constrained molecular dynamics (MD) studies, such that predictions may be made about conjugates not yet synthesized. Focusing on two B12 conjugates of the anorectic peptide PYY(3–36), one of which was previously demonstrated to have improved food intake reduction compared with PYY(3–36), we performed NMR structural analyses and used the information to conduct MD simulations. The study provides rare structural insight into vitamin B12 conjugates and validates the fact that B12 can be conjugated to a peptide without markedly affecting peptide secondary structure.
Published earlier this year in RSC Advances (RSC Adv., 2013, 3, 19081-19096), a follow-up (for my part) to the study The Low-/Room-temperature Forms Of The Lithiated Salt Of 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone: A Combined Experimental And Dispersion-Corrected Density Functional Study in CrystEngComm last year. The theoretical section for this paper is a tour-de-force of Crystal09 solid-state optimizations, density functional and dispersion-correction dependence, and post-processing using Carlo Gotti’s TOPOND software. In brief, the combination of vibrational spectra, electochemical measurements, and solid-state density functional theory tests are used to predict the structure of the previously unknown lithiated tetramethoxy-p-benzoquinone structure based on the good-to-excellent agreement with two known TMQ crystal structures (the testing of density functionals and dispersion corrections being a very good survey of the pros and cons of the varied methods. If you were pondering an approach to follow to perform the same kind of theoretical analysis, the procedure set up by Gaëtan and Christine in this paper is fully worth your consideration).
Gaëtan Bonnard, Anne-Lise Barrès, Yann Danten, Damian G. Allis, Olivier Mentré, Daniele Tomerini, Carlo Gatti, Ekaterina I. Izgorodina, Philippe Poizot and Christine Frayret*
In the search for low-polluting electrode materials for batteries, the use of redox-active organic compounds represents a promising alternative to conventional metal-based systems. In this article we report a combined experimental and theoretical study of tetramethoxy-p-benzoquinone (TMQ). In carbonate-based electrolytes, electrochemical behaviour of this compound is characterized by a reversible insertion process located at approximately 2.85 V vs. Li+/Li0. This relatively high potential reactivity, coupled with our effort to develop computational methodologies in the field of organic electrode materials, prompted us to complement these experimental data with theoretical studies performed using density functional theory (DFT). Single crystals of TMQ were synthesized and thoroughly characterized showing that this quinonic species crystallised in the P21/n space group. The experimental crystal structure of TMQ was then used to assess various DFT methods. The structural features and vibrational spectra were thus predicted by using as a whole five common density functionals (PBE, LDA, revPBE, PBEsol, B3PW91) with and without a semi-empirical correction to account for the van der Waals interactions using either Grimme’s (DFT-D2) or Tkatchenko–Scheffler (TS) scheme. The most reliable combination of the DFT functional and the explicit dispersion correction was chosen to study the Li-intercalated molecular crystal (LiTMQ) with the view of indentifying Li insertion sites. A very close agreement with the experiment was found for the average voltage by using the most stable relaxed hypothetical LiTMQ structure. Additionally, a comparison of vibrational spectra gained either for TMQ molecule and its dimer in gas phase or through periodic calculation was undertaken with respect to the experimentally measured infrared spectra. The topological features of the bonds were also investigated in conjunction with estimates of net atomic charges to gain insight into the effect of chemical bonding and intermolecular interaction on Li intercalation. Finally, π-electron delocalization of both quinone and alkali salts of p-semiquinone were determined using the Harmonic Oscillator model of Aromaticity (HOMA) or aromatic fluctuation index (FLU) calculations.
Published in Crystal Growth & Design (Cryst. Growth Des., 2013, 13 (9), pp. 3852–3855) earlier this year. The theory work is less impressive than the successful crystal growth, with initial solid-state efforts in Crystal09 only very recently now producing good results (leaving the molecular calculations to Gaussian09 in this paper). The procedure leading to the observed crystal structure of this inclusion complex is a significant step in the direction of testing the theory proposed in Bond Alternation In Infinite Periodic Polyacetylene: Dynamical Treatment Of The Anharmonic Potential published earlier this year in J. Mol. Struct.
Caption: Two views along the ba and ca crystal axes of the (E,E)‐1,4-Diiodo-1,3-Butadiene : Urea Inclusion Complex.
Amanda F. Lashua, Tiffany M. Smith, Hegui Hu, Lihui Wei, Damian G. Allis, Michael B. Sponsler, and Bruce S. Hudson
Abstract: The urea inclusion compound (UIC) with (E,E)-1,4-diiodo-1,3-butadiene (DIBD) as a guest (DIBD:UIC) has been prepared and crystallographically characterized at 90 and 298 K as a rare example of a commensurate, fully ordered UIC. The crystal shows nearly hexagonal channels in the monoclinic space group P21/n. The DIBD guest molecules are arranged end-to-end with the nonbonding iodine atoms in the van der Waals contact. The guest structure is compared with that for DIBD at 90 K and with computations for the periodic UIC and isolated DIBD molecule.
As first appeared on the CNY Observers & Observing website, www.cnyo.org, on 22 June 2013.
Greetings fellow astrophiles!
As if NEAF wasn’t already an excellent first showing for Ryan (and Heather!) Goodson and New Moon Telescopes (including discussions at Cloudy Nights (link 1, link 2) and a recorded observation in Sky & Telescope in this month’s issue), I am pleased to provide a full copy of the result of their first NEAF meeting with Gary Parkerson, Managing Editor of Astronomy Technology Today (www.astronomytechnologytoday.com): A feature (and cover) article (by yours truly) giving the NMT 16″ f/4.5 Dobsonian a complete walk-through in the May-June 2013 issue.
Continue reading “The 16-inch f/4.5 Collapsible-Truss Dobsonian From New Moon Telescopes – Feature Article In Astronomy Technology Today”
The back cover picture shows two views at 150 degree rotation of vitamin B12 conjugated to the potent anti- hyperglycemia peptide glucagon-like peptide-1 (GLP-1). The conjugate displays similar receptor binding and agonism to unconjugated GLP-1, including insulin potentiation from human transplant pancreatic islet cells, which bodes well for oral delivery of GLP-1 through the B12 dietary pathway. For more details, see the Communication by Robert P. Doyle et al. on p. 582 ff.
From the free press department… The cover for the April, 2013 issue of ChemMEDChem (just the cover art this time, no theoretical content in the associated article. All the theory’s figured out!). I’m still awaiting the journal’s posting of the article content but wanted to get something up in March. For related content, see the discussion on the “MedChemComm September 2012 Front Cover Image For The ‘Examining The Effects Of Vitamin B12 Conjugation…’ Paper” post or any of the B12-related posts on this site (www.somewhereville.com/index.php?s=b12). This work is similar in scope to the B12-insulin bioconjugate work in the previous studies, but now includes a different peptide (glucagon-like peptide-1) with similar properties.
In press, in CrystEngComm (DOI:10.1039/C2CE26523). This is my first full paper completely internet-powered, in that I’ve not physically met any of the other co-authors (also in the internet-powered context, the recent paper on -annulene was written and submitted without sharing a room with Dr. Bruce Hudson, but we’re in the same building, so it doesn’t quite count). Also, one of the few papers for which I had no image generation duties (a rare treat).
The discussion of the very interesting possibilities of molecular redox materials in lithium-ion batteries aside, this paper presents a very thorough example of the power of computational approaches to greatly improve the understanding of solid-state molecular materials by (specifically) 1: overcoming the hydrogen position identification problems inherent in X-ray diffraction methods, 2: reproducing the changes that come with temperature variations in molecular crystals and explaining the origins of those (possibly subtle) changes by way of dispersion-corrected density functional theory, and 3: demonstrating that the nature of intermolecular interactions (specifically hydrogen bonding) can be rigorously cataloged across varied materials using post-optimization tools (in this case, using Carlo Gatti’s excellent TOPOND program).
Caption: Issue cover.
Gaëtan Bonnard, Anne-Lise Barrès, Olivier Mentré, Damian G. Allis, Carlo Gatti, Philippe Poizot and Christine Frayret*
Following our first experimental and computational study of the room temperature (RT) form of the tetrahydrated 3,6-dihydroxy-2,5-dimethoxy-p-benzoquinone (LiM2DHDMQ⋅4H2O) compound, we have researched the occurrence of hydrogen ordering in a new polymorph at lower temperature. The study of polymorphism for the Li2DHDMQ⋅4H2O phase employs both experimental (single crystal X-ray diffraction) and theoretical approaches. While clues for disorder over one bridging water molecule were observed at RT (beta-form),a fully ordered model within a supercell has been evidenced at 100K (alpha-form) and is discussed in conjunction with the features characterizing the first polymorphic form reported previously. Density functional theory (DFT) calculations augmented with an empirical dispersion correction (DFT-D) were applied for the prediction of the structural and chemical bonding properties of the alpha and beta polymorphs of Li2DHDMQ·4H2O. The relative stability of the two polymorphic systems is evidenced. An insight into the interplay of hydrogen bonding, electrostatic and van der Waals (vdW) interactions in affecting the properties of the two polymorphs is gained. This study also shows how information from DFT-D calculations can be used to augment the information from the experimental crystal diffraction pattern and can so play an active role in crystal structure determination, especially by increasing the reliability and accuracy of H-positioning. These more accurate hydrogen coordinates allowed for a quantification of H-bonding strength through a topological analysis of the electron density (Atoms-in-molecules theory).
Blogging a blog post recently blogged here in a post, with a zoom-in below because no decent-sized version of the same can be found on the MedChemComm site, all pertaining to the “Examining the effects of vitamin B12 conjugation on the biological activity of insulin: a molecular dynamic and in vivo oral uptake investigation” article from Susan Clardy-James, myself, Timothy J. Fairchild and Robert P. Doyle in ChemMedComm (available at pubs.rsc.org/en/Content/ArticleLanding/2012/MD/C2MD20040F).
The MedChemComm post also provides the caption for the cover (below), which I reproduce below for context:
Oral delivery of drugs aims to open up new areas of peptide/protein therapeutics associated with the removal for a need for injections. The major problems facing oral delivery of peptides/proteins is hydrolysis/proteolysis in the gastrointestinal tract and an inefficient uptake mechanism for peptides/proteins from the tract. Robert P. Doyle et al. are interested in the use of the vitamin B12 dietary uptake pathway to address these hurdles. In this paper Doyle et al. report the synthesis, purification and characterisation of a new B12-insulin conjugate attached between the B12 ribose hydroxyl group and insulin PheB1.
In press (DOI:10.1016/j.molstruc.2012.07.051) in the Journal Of Molecular Structure. May go down in history as a hardest-fought paper acceptance. In a similar line of research as the -annulene study, but exploring the infinite limit of geometry and bond length alternation energy barrier for this infinite case. If the numbers are correct, the infinite polyene chains (polyacetylene) do not exhibit bond length alternation because the Peierls’ barrier between the single-double and double-single bond alternate minima is below the vibrational zero-point level. Plenty of ramifications.
Bruce S. Hudson and Damian G. Allis
Abstract. The potential energy of the infinite periodic chain model of polyacetylene (pPA) is symmetric with two equivalent minima separated by the Peierls’ stabilization barrier. In this work it is shown how an energy scale and vibrational energy levels for this highly anharmonic Peierls’ degree of freedom can be estimated. Attention is given to the potential energy increase for large deformations. The Born-Kármán treatment of translational symmetry is applied. Two empirical methods and a direct periodic boundary condition (PBC) density functional theory (DFT) calculations are in semi-quantitative agreement, each leading to the conclusion that pPA has a zero-point level that is above the Peierls’ barrier. The argument does not depend critically on the barrier height or the other parameters of the model or the computation method. It is concluded that pPA will not exhibit bond alternation and that the zero-point average geometry does not preclude possible conductivity.
In press (DOI:10.1016/j.molstruc.2012.05.016) in the Journal Of Molecular Structure (Volume 1023, 12 September 2012, Pages 212–215) in the special issue: MOLECULAR VIBRATIONS AND STRUCTURES: THEORY AND EXPERIMENT — A collection of papers dedicated to Professor Jaan Laane on the occasion of his 70th birthday.
This paper on the “actual” geometry of -annulene is part of several larger stories addressing a larger polyene (or larger-polyene) issue. First among these is the meaning of experimental results obtained by various spectroscopic methods (in this case, using previous X-ray, Raman (with the C2 (blue) and D6h (red) simulated spectra shown in the image above), IR, and NMR data that produce different results within the limitations of the methods to study the single molecule). Second is the quality of the theoretical method for reproducing certain types of spectroscopic data. In the case of the [N]-annulene series, the ever-present B3LYP density functional is found to produce the time-average geometry of -annulene found in X-ray data, but another density functional (in this case, KMLYP), finds that bond-alternate minima exist. Third is the importance of the zero-point level in the treatment of systems for which bond-alternate geometries exist with transition-state barriers calculated to be below the zero-point level in the classical approximation of nuclear positions (the Born-Oppenheimer Approximation).
NOTE 1: The KMYLP density functional is called in Gaussian with the following keyword set:
BLYP iop(3/76=1000005570) iop(3/77=0000004430) iop(3/78=0448010000)
NOTE 2: Optimization and Frequency calculations must be performed as TWO SEPARATE CALCULATIONS. The iop-called density functional does not carry itself over between opt + freq (or other properties) in the same input file. If you opt + freq in the same input file, you will Opt with KMLYP but freq with BLYP. This will be obvious by the number of imaginary modes.
Bruce S. Hudson and Damian G. Allis
Abstract. -annulene has been of great interest from the structural point of view of its bond alternation. High-level calculations based on structures selected for agreement with NMR spectra lead to a bond-alternate C2 form over a non-alternating planar D6h structure deduced from diffraction, infrared (IR) and electronic spectral studies. Here it is shown that computed Raman spectra for the D6h and C2 forms are expected to be very different. However, two equivalent non-D6h bond-alternate minima of D3h or C2 geometries are separated by only a small barrier along a motion that involves CC stretching and compression. It is shown here that the zero-point level is above the barrier for this species. In light of that fact, the NMR calculations are reconsidered with inclusion of zero-point level averaging.
As first appeared in the May 2012 edition of the Syracuse Astronomical Society newsletter The Astronomical Chronicle.
Image generated with Starry Night Pro 6.
We return to our circumpolar constellation discussion begun with the Jan/Feb/March 2012 issue (our first “quarterly” report) by scaling up the Northern Horizon towards Draco the Dragon.
Draco, like all reptiles, is a bit on the dim side. Most of its constituent stars are in the 3 to 4.5 Magnitude range, making it an easy target in dark skies but a bit of a hunt near larger cities. If you’ve never looked for it before, it rivals Ursa Minor (the Little Dipper) in terms of “meh” apparent brightness in the sky (so it is far less pronounced than the Big Dipper or Cassiopeia, the two most prominent Constellations in this part of the sky).
Continue reading “Some Light Science Reading. The Constellations: Draco”