Ab-initio Carbon Capture in Open-Site Metal Organic Frameworks

During the formation of metal–organic frameworks (MOFs), metal centres can coordinate with the intended organic linkers, but also with solvent molecules. In this case, subsequent activation by removal of the solvent molecules creates unsaturated ‘open’ metal sites known to have a strong affinity for CO2 molecules, but their interactions are still poorly understood. Common force fields typically underestimate by as much as two orders of magnitude the adsorption of CO2 in open-site Mg-MOF-74, which has emerged as a promising MOF for CO2 capture. Here we present a systematic procedure to generate force fields using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field generated for CO2 in Mg-MOF-74 shed some light on the interpretation of thermodynamic data from flue gas in this material. The force field describes accurately the chemistry of the open metal sites, and is transferable to other structures. This approach may serve in molecular simulations in general and in the study of fluid–solid interactions

Density functional theory of molecular conductivity

This thesis is about current-density functional theory. Current plays a role in three important types of physical systems: molecular electronic devices (MED), broken current-symmetry states of atoms and molecules, and states of atoms and molecules in external magnetic fields. Developments in these three areas of current-density functional theory are presented in this thesis. First, the thesis proposes an extension of conventional density functional theory that accounts for the direct current flow through a MED under a voltage bias. The irreversible current flow in a MED is introduced by coupling the MED to a pair of reservoirs at two distinct local equilibria. This coupling defines a model non-Hermitian Hamiltonian whose eigenfunctions correspond to the coherent current carrying modes of the MED. A stationarity principle for the irreversible state of MED is constructed that resembles the variational principle of conventional quantum mechanics. As an application of the stationarity principle, a generalization of Kohn-Sham density functional theory suitable for MEDs is derived. The developed current density functional theory is applied to a di-thiol benzene molecule under a voltage bias. The new approach agrees with the established non-equilibrium Green's functions method. Second, this thesis develops an approximate functional that accounts for the current dependence of the exchange-correlation energy in systems with broken current symmetry. Starting from the Perdew-Burke-Ernzerhof generalized gradient approximation, first principle conditions are employed to built a non-empirical exchange functional. Matching the correlation functional to that for exchange yields a current-dependent approximation for correlation. The resulting functional is given in a simple closed form. The benchmark of this functional against the broken current symmetry ground-states of open shell atoms indicates an improvement, as compared to the current-independent generalized gradient approximations. Third, this thesis presents a current-dependent approach to magnetic response properties of atoms and molecules. The NMR shielding tensors computed for a benchmark set of molecules indicate a superiority of the novel approach over the common generalized gradient approximations and hybrid functionals for strongly deshielded nuclei

Redox chemistry and metal-insulator transitions intertwined in a nano-porous material

Metal organic frameworks are nano porous adsorbents of relevance to gas separation and catalysis, and O2 separation from air is essential to diverse industrial applications. A metal organic framework Fe2(DOBDC), also known as a MOF74, can selectively adsorb O2 in a manner that defies the classical picture: Adsorption sites either do or do not share electrons over a long range. This report proposes, and then justifies phenomenologically and computationally, a mechanism. Charge transfer mediated adsorption of an electron acceptor O2 in a quasi one dimensional (1D) electron donor semiconductor Fe2(DOBDC) drives and is driven by 1D metal insulator transitions that localize or delocalize the 1D electrons. This mechanism agrees with the empirical evidence, and predicts a class of nano porous semiconductors or metals and potential adsorbents and catalysts in which chemistry and metal insulator transitions intertwine.Comment: This paper has been withdrawn by the authors as it represented an incomplete descriptio

Chemistry of fast electrons

A chemicurrent is a flux of fast (kinetic energy ≳ 0.5−1.3 eV) metal electrons caused by moderately exothermic (1−3 eV) chemical reactions over high work function (4−6 eV) metal surfaces. In this report, the relation between chemicurrent and surface chemistry is elucidated with a combination of top-down phenomenology and bottom-up atomic-scale modeling. Examination of catalytic CO oxidation, an example which exhibits a chemicurrent, reveals 3 constituents of this relation: The localization of some conduction electrons to the surface via a reduction reaction, 0.5 O2 + δe− → Oδ− (Red); the delocalization of some surface electrons into a conduction band in an oxidation reaction, Oδ− + CO → CO2δ− → CO2 + δe− (Ox); and relaxation without charge transfer (Rel). Juxtaposition of Red, Ox, and Rel produces a daunting variety of metal electronic excitations, but only those that originate from CO2 reactive desorption are long-range and fast enough to dominate the chemicurrent. The chemicurrent yield depends on the universality class of the desorption process and the distribution of the desorption thresholds. This analysis implies a power-law relation with exponent 2.66 between the chemicurrent and the heat of adsorption, which is consistent with experimental findings for a range of systems. This picture also applies to other oxidation-reduction reactions over high work function metal surfaces

DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study

Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson–Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson–Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson–Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis

Liaison préférentielle de O2 sur N2 dans un réseau métal-organique actif en redox avec des sites ouverts de coordination de fer(II).

The air-free reaction of FeCl2 and H4dobdc (dobdc4- = 2,5-dioxido-1,4- benzenedicarboxylate) in a mixture of DMF and methanol affords Fe2(dobdc), a metal-organic framework isostructural to M2(dobdc) (M = Mg2+, Mn2+, Co2+, Ni2+, Zn2+). The desolvated form of this material has a BET surface area of 1360 m2/g and features 1-D hexagonal pores lined with coordinatively unsaturated Fe2+ cations. O2 adsorption isotherms indicate Fe2(dobdc) irreversibly binds oxygen at 298 K at a capacity over 0.10 mass fraction, corresponding to the adsorption of one O2 molecule per two framework Fe2+ cations. Remarkably, O2 uptake is reversible and the capacity increases two-fold to 0.19 mass fraction at 211 K. Powder neutron diffraction and IR spectroscopy indicate that in both scenarios O2 is coordinated side-on to the iron centers as superoxide at low temperatures and peroxide at room temperature, an observation that is confirmed by Mössbauer spectroscopy. Ideal adsorbed solution theory calculations reveal that Fe2(dobdc) is a promising material for the separation of O2 from air at temperatures well above those currently used in industrial settings