Coordinates of Molecular Clusters: See relevant paper for details



Quantum chemical study of the structure, spectroscopy and reactivity of NO+.(H2O)n=1-5 clusters.
K.A. Linton, T.G. Wright and N.A. Besley
Phil. Trans. Roy. Soc. Lond., 376, 20170152 (2018)
Abstract
Quantum chemical methods including Møller–Plesset perturbation (MP2) theory and density functional theory (DFT) have been used to study the structure, spectroscopy and reactivity of NO+.(H2O)n=1−5 clusters. MP2/6-311++G** calculations are shown to describe the structure and spectroscopy of the clusters well. DFT calculations with exchange–correlation functionals with a low fraction of Hartree–Fock exchange give a binding energy of NO+.(H2O) that is too high and incorrectly predict the lowest energy structure of NO+.(H2O)2, and this error may be associated with a delocalization of charge onto the water molecule directly binding to NO+. Ab initio molecular dynamics (AIMD) simulations were performed to study the NO+.(H2O)5 → H+.(H2O)4 + HONO reaction to investigate the formation of HONO from NO+.(H2O)5. Whether an intracluster reaction to form HONO is observed depends on the level of electronic structure theory used. Of note is that methods that accurately describe the relative energies of the product and reactant clusters did not show reactions on the timescales studied. This suggests that in the upper atmosphere the reaction may occur owing to the energy present in the NO+.(H2O)5 complex following its formation.

no
Cluster Coordinates



Infrared Spectroscopy of NaCl(CH3OH)n complexes in helium nanodroplets.
A. Sadoon, G. Sarma, E.M. Cunningham, J. Tandy, M.W.D. Hanson-Heine, N.A. Besley, S. Yang and A.M. Ellis
J. Phys. Chem. A, 120, 8085-8092 (2016)
Abstract
Infrared (IR) spectra of complexes between NaCl and methanol have been recorded for the first time. These complexes were formed in liquid helium nanodroplets by consecutive pick-up of NaCl and CH3OH molecules. For the smallest NaCl(CH3OH)n, complexes where n = 1−3, the IR data suggest that the lowest-energy isomer is the primary product in each case. The predominant contribution to the binding comes from ionic hydrogen bonds between the OH in each methanol molecule and the chloride ion in the NaCl, as established by the large red shift of the OH stretching bands compared with the isolated CH3OH molecule. For n ≥ 4, there is a dramatic shift from discrete vibrational bands to very broad absorption envelopes, suggesting a profound change in the structural landscape and, in particular, access to multiple low-energy isomers.

ellis
Cluster Coordinates



Spectroscopic and structural analysis of mixed carbon dioxide and fluorinated methane clusters.
M. W. D. Hanson-Heine and N. A. Besley
Chem. Phys. Lett., 638, 191-195 (2015)
Abstract
The minimum energy structures and corresponding infrared spectra of molecular clusters containing pure carbon dioxide, (CO2)n (n = 2-5), together with mixed clusters containing both carbon dioxide and either methane, fluoromethane, difluoromethane, trifluoromethane, or tetrafluoromethane , CH4(CO2)n , CH3F(CO2)n, CH2F2(CO2)n, CHF3(CO2)n, CF4(CO2)n (n = 1-5), have been studied using a basin hopping search technique combined with ab initio energies and gradients. Basin hopping searches in conjunction with density functional theory with empirical (B3LYP+D) dispersion corrections and second order Møller-Plesset perturbation theory (MP2) yield qualitatively similar minimum energy configurations for pure carbon dioxide clusters. The structure and infrared vibrational spectra of the fluorinated methane containing clusters show a dominant factor is the attraction between the carbon atom of carbon dioxide and the fluorine atoms.

co2
Cluster Coordinates

The structure and bonding of mixed component radical cation clusters.
J. D. Wadey and N.A. Besley
Chem. Phys. Lett., 601, 110-115 (2014)
Abstract
Basin hopping in conjunction with second order Møller-Plesset perturbation theory is used to characterise the lowest energy isomers of mixed component radical cation clusters of the form [H2O-X]+, [(H2O)2-X]+ and [H2O-X2]+, where X=PH3, H2S and HCl, with the relative energies refined using coupled cluster theory calculations. For the dimers where X=H2S or HCl, a proton transfer based structure comprising H3O+ and SH or Cl radicals has the lowest energy structure whereas for X=PH3 a hemibonded structure is most stable. For the trimers, a much wider range of possible isomers based upon both proton transfer and hemibonded structural motifs is observed.

mixed
Cluster Coordinates



Proton transfer or hemibonding? The structure and stability of radical cation clusters.
H. Do and N.A. Besley
Phys. Chem. Chem. Phys., 15, 16214-16219 (2013)
Abstract
The basin hopping search algorithm in conjunction with second-order Møller-Plesset perturbation theory is used to determine the lowest energy structures of the radical cation clusters (NH3)n+, (H2O)n+, (HF)n+, (PH3)n+, (H2S)n+ and (HCl)n+, where n=2-4. The energies of the most stable structures are subsequently evaluated using coupled cluster theory in conjunction with the aug-cc-pVTZ basis set. These cationic clusters can adopt two distinct structural types, with some clusters showing an unusual type of bonding, often referred to as hemibonding, while other clusters undergo proton transfer to give an ion and radical. It is found that proton transfer based structures are preferred by the (NH3)n+, (H2O)n+, (HF)n+ clusters while hemibonded structures are favoured by (PH3)n+, (H2S)n+ and (HCl)n+. These trends can be attributed to the relative strengths of the molecules and molecular cations as Brønsted bases and acids, respectively, and the strength of the interaction between the ion and radical in the ion-radical clusters.

hemibonding
Cluster Coordinates


Structure and bonding in ionized water clusters.
H. Do and N.A. Besley
J. Phys. Chem. A, 117, 5385-5391 (2013)
Abstract
The structure and bonding in ionized water clusters, (H2O)n+ (n=3-9), has been studied using the basin hopping search algorithm in combination with quantum chemical calculations. Initially candidate low energy isomers are generated using basin hopping in conjunction with density functional theory. Subsequently, the structures and energies are refined using second order Moller-Plesset perturbation theory and coupled cluster theory, respectively. The lowest energy isomers are found to involve proton transfer to give H3O+ and a OH radical, which are more stable than isomers containing the hemibonded hydrazine-like fragment (H2O--OH2), with the calculated infrared spectra consistent with experimental data. For (H2O)9+ the observation of a new structural motif comprising proton transfer to form H3O+ and OH, but with the OH radical involved in hemibonding to another water molecule is discussed.

cation
Cluster Coordinates


Structural optimization of molecular clusters with density functional theory combined with basin hopping.
H. Do and N.A. Besley
J. Chem. Phys., 137, 134106 (2012)
Abstract
Identifying the energy minima of molecular clusters is a challenging problem. Traditionally, search algorithms such as simulated annealing, genetic algorithms or basin hopping are usually used in conjunction with empirical force fields. We have implemented a basin hopping search algorithm combined with density functional theory to enable the optimization of molecular clusters without the need for empirical force fields. This approach can be applied to systems where empirical potentials are not available or may not be sufficiently accurate. We illustrate the effectiveness of the method with studies on water, methanol and water + methanol clusters as well as protonated water and methanol clusters at the B3LYP+D/6-31+G* level of theory. A new lowest energy structure for H+(H2O)7 is predicted at the B3LYP+D/6-31+G* level. In all of the protonated mixed water and methanol clusters, we find that H+ prefers to combine with methanol rather than water in the lowest-energy structures.
jcp1
jcp2
Cluster Coordinates