Chapter published in Annual Reports on NMR Spectroscopy

17O NMR as a Tool in Discrete Metal Oxide Cluster Chemistry

in Annual Reports on NMR Spectroscopy. Link.

C. André Ohlin, William H. Casey

Abstract: This chapter covers recent developments in 17O NMR spectroscopy as applied to discrete metal oxide clusters, particularly in the context of their use as models in geochemistry and catalysis. Dynamic 17O NMR methods based on the McConnell–Bloch equations are explored in depth, and recent advances are reviewed. High-pressure NMR methods are also discussed and reviewed, as are recent developments in the use of density functional theory in the computation of 17O NMR shifts in polyoxometalates. The emphasis of the chapter is on the new developments that promise to reinvigorate 17O NMR as a central tool in the study of aqueous chemical kinetics, with the most urgent challenges being understanding the rates of isotopic substitution into bridging oxygens in clusters.

Paper on fractionation accepted by Geochimica et Cosmochimica Acta

Computational Prediction of Mg-Isotope Fractionation Between Aqueous [Mg(OH2)6]2+ and Brucite

Geochim. Cosmochim. Acta., Accepted. Link.

Christopher A. Colla, W. H. Casey, C. André Ohlin

Abstract: The fractionation factor in the magnesium-isotope fractionation between aqueous solutions of magnesium and brucite remarkably changes sign with increasing temperature, as uncovered by recent experiments.  To understand this behavior, the Reduced Partition Function Ratios and isotopic fractionation factors (Δ26/24Mgbrucite-Mg(aq)) are calculated using molecular models of aqueous [Mg(OH2)6]2+ and the mineral brucite at increasing levels of density functional theory.  The calculations were carried out on the [Mg(OH2)6]2+·12H2O cluster, along with different Pauling-bond-strength-conserving models of the mineral lattice of brucite. Three conclusions were reached: i) all of the calculations overestimate <Mg-O> bond distances in the aqua ion complex relative to Tutton’s salts; ii) the calculations predict that brucite at 298.15 K is always enriched in the heavy isotope, in contrast with experimental observations; iii) the temperature dependencies of Wimpenny et al. (2014) and Li et al. (2014) could only be achieved by fixing the <Mg-O> bond distances in the [Mg(OH2)6]2+·12H2O cluster to values close to those observed in crystals that trap the hydrated ion. Read more.

 

Paper accepted by Dalton Trans.

PNacPNacE: (E = Ga, In, Tl) – monomeric group 13 metal(I) heterocycles stabilized by a sterically demanding bis(iminophosphoranyl)methanide

Dalton Trans., 2017, 46, 16872-16877.

Christian P. Sindlinger, Samuel R. Lawrence, Shravan Acharya, C. André Ohlin, Andreas Stasch

Abstract: The salt metathesis reaction of the sterically demanding bis(iminophosphoranyl)methanide alkali metal complexes LM (L – = HC(Ph 2 P=NDip) 2- , Dip = 2,6- i Pr 2 C 6 H 3 ; M = Li, Na, K) with “GaI”, InBr or TlBr afforded the monomeric group 13 metal(I) complexes LE:, E = Ga (1), In (2) and Tl (3), and small quantities of LGaI 2 4 in case of Ga, respectively. The molecular structures of LE: 1-3 from X-ray single crystal diffraction show them to contain puckered six-membered rings with N,N’-chelating methanide ligands and two-coordinated metal(I) centres. Reduction reactions of LAlI 2 5, prepared by iodination of LAlMe 2 , were not successful and no aluminium(I) congener could be prepared so far. DFT studies on LE:, E = Al–Tl, were carried out and support the formulation as an anionic, N,N’-chelating methanide ligand coordinating to group 13 metal(I) cations. The HOMOs of the molecules for E = Al-In show a dominant contribution from a metal-based lone pair that is high in s-character. See http://pubs.rsc.org/en/content/articlelanding/2017/dt/c7dt04048b#!divAbstract

What to use?

In my group we use linux exclusively. This is done for a number of reasons, chief of which are that it works best with the best tools for our work, and because I can provide you with limited IT support if you are using Linux. Any other OS and you’re on your own.

So here’s a list of tools that we use on linux and what we use them for:

Writing — latex when possible, libreoffice when not, and WPS when we must deal with office documents.

Spreadsheets — gnumeric (always ask yourself whether a spreadsheet is a good idea — often sed/gawk is better)

Plotting and fitting — gnuplot

Simulation/general maths — Octave

Programming — Python (2.7)

Computational chemistry framework — ECCE

CAS — Maxima

File sharing — UMU has 1 Tb storage for each staff member on One Drive via Office 365, so while it’s not great on linux, this is what we use.

 

 

Use those iptables…

If you can’t rely on your local network being firewalled the onus is on you to make sure that you have a firewall running on your computer. On linux you have iptables, which is remarkably easy to use if you have at least a basic understanding of how networking works (and/or google). Without going into details, you REALLY, REALLY. REALLY need to have your OWN firewall running if you are based at Umeå University.

Your needs may vary, but here’s a script that you can put in e.g. /etc/firewall_rules.sh

Have it called from /etc/rc.local so that it starts during boot.

#!/bin/sh
sudo iptables -F #FLUSH
#INPUT
sudo iptables -A INPUT -m conntrack –ctstate ESTABLISHED,RELATED -j ACCEPT #allows network
sudo iptables -A INPUT -i lo -j ACCEPT #127.0.0.1
sudo iptables -A INPUT -s 127.0.0.1 -j ACCEPT
sudo iptables -A INPUT -p tcp –dport ssh -j ACCEPT #ssh -world!
sudo iptables -A INPUT -p icmp –icmp-type 8 -j ACCEPT -s 192.168.1.0/24 #ping
sudo iptables -A INPUT -d 255.255.255.255 -j ACCEPT #broadcast traffic
sudo iptables -A INPUT -m limit –limit 15/minute -j LOG –log-level 7 –log-prefix ” Dropped by firewall ”
sudo iptables -A INPUT -m limit –limit 15/minute -j LOG –log-level 4 –log-prefix “[netfilter]”
sudo iptables -A INPUT -j DROP #drop all else
#OUTPUT
sudo iptables -A OUTPUT -o lo -j ACCEPT #127.0.0.1
sudo iptables -A OUTPUT -j ACCEPT #all outgoing ok
#FORWARD
sudo iptables -A FORWARD -p icmp –icmp-type 8 -j ACCEPT
#Default behaviour
sudo iptables -P INPUT DROP
sudo iptables -P OUTPUT DROP
sudo iptables -P FORWARD DROP
exit 0

ECCE forked, hosted at https://github.com/FriendsofECCE/ECCE

The PNNL developed a Linux code called ECCE (Extensible Computational Chemistry Environment; http://ecce.emsl.pnl.gov/) in the 90s and 00s. Unfortunately, no more resources seem to be made available to maintain the code.

This is a shame since it has some interesting functionality:

  • can be used to prepare input files for gaussian and nwchem
  • can submit jobs either directly or to queue managers (SGE, Slurm)
  • can open and visualise the output

And on top of this it’s open source and runs on Linux.

I and Matt Asplund of BYU have thus decided to try to develop a community maintained version. We have put this at https://github.com/FriendsofECCE/ECCE

In addition to maintaining the code, we also have three standard build environment for which we release precompiled binaries.

You can thus download binaries for Centos 7, Ubuntu LTS 16.04.2 and Debian 8.8, in addition to the source code.

Currently there are three release versions:

7.0 — The unmodified PNNL code

7.0.1 — The PNNL code modified to allow it to compile without any further patching on CentOS, Ubuntu and Debian

7.1.0 — A heavily modified version of the PNNL code that introduces new functionality and fixes old bugs