Salinity and pH effects on water-oil-calcite interfaces by using molecular dynamics.

Smart water injection is a technology that allows changing the wettability of the oil rock by injecting water at different salinities, in a cheap and environmentally friendly way compared to other traditional methods. In this study, the individual effect of some typical salts on the wettability of the (104) surface of calcite toward non-polar and polar crude oil models was explored by molecular dynamics as a function of the salinity and pH. The results obtained show that the electrical double layer plays a principal role in the detachment of crude oil models. The divalent ion salts, i.e., CaCl2, CaSO4, MgCl2, and MgSO4, do not form the electrical double layer on calcite, but salts of NaCl and Na2SO4 form it. Moreover, the surface affinity of calcite to the non-polar crude oil is not affected by the salinity. However, the affinity of the calcite surface toward polar crude is affected by salinity and pH conditions. This research provides new insights into the action mechanisms that could help optimize its uses in enhanced oil recovery.

Outstanding improvement in removing the delocalization error by global natural orbital functional.

This work assesses the performance of the recently proposed global natural orbital functional (GNOF) against the charge delocalization error. GNOF provides a good balance between static and dynamic electronic correlations leading to accurate total energies while preserving spin, even for systems with a highly multi-configurational character. Several analyses were applied to the functional, namely, (i) how the charge is distributed in super-systems of two fragments, (ii) the stability of ionization potentials while increasing the system size, and (iii) potential energy curves of a neutral and charged diatomic system. GNOF was found to practically eliminate the charge delocalization error in many of the studied systems or greatly improve the results obtained previously with PNOF7.

Electron Correlation in the Iron(II) Porphyrin by Natural Orbital Functional Approximations.

The relative stability of the singlet, triplet, and quintet spin states of iron(II) porphyrin (FeP) represents a challenging problem for electronic structure methods. While it is currently accepted that the ground state is a triplet, multiconfigurational wave function-based methods predict a quintet, and density functional approximations vary between triplet and quintet states, leading to a prediction that highly depends on the features of the method employed. The recently proposed Global Natural Orbital Functional (GNOF) aims to provide a balanced treatment between static and dynamic correlation, and together with the previous Piris Natural Orbital Functionals (PNOFs), allowed us to explore the importance of each type of correlation in the stability order of the states of FeP with a method that conserves the spin of the system. It is noteworthy that GNOF correlates all electrons in all available orbitals for a given basis set; in the case of the FeP with a double-ζ basis set as used in this work, this means that GNOF can properly correlate 186 electrons in 465 orbitals, significantly increasing the sizes of systems amenable to multiconfigurational treatment. Results show that PNOF5, PNOF7s, and PNOF7 predict the quintet to have a lower energy than the triplet state; however, the addition of dynamic correlation via second-order Møller-Plesset corrections (NOF-MP2) turns the triplet state to be lower than the quintet state, a prediction also reproduced by GNOF that incorporates much more dynamic correlation than its predecessors.

Wettability of graphene oxide functionalized with N-alkylamines: a molecular dynamics study.

The wettability of graphene oxide functionalized with N-alkylamines was studied by molecular dynamics simulations. Six different N-alkylamines and two functionalization degrees were reviewed. The nucleophilic ring-opening reaction mechanism between the N-alkylamines and epoxy functional groups of graphene oxide was considered to generate the atomistic models. Water contact angles increased with both the alkyl chain length and substitution degree. The Wenzel model was used to access the effect of both the surface roughness and alkyl chain length on wettability. The results indicated that functionalization introduces an important increase of surface roughness but its effect on wettability is countered by the alkyl chain length.

Self-Consistent Auxiliary Density Perturbation Theory.

The working equations for the extension of auxiliary density perturbation theory (ADPT) to hybrid functionals, employing the variational fitting of the Fock potential, are derived. The response equations in the resulting self-consistent ADPT (SC-ADPT) are solved iteratively with an adapted Eirola-Nevanlinna algorithm. As a result, a memory and CPU time efficient implementation of perturbation theory free of four-center electron repulsion integrals (ERIs) is obtained. Our validation calculations of SC-ADPT static and dynamic polarizabilities show quantitative agreement with corresponding coupled perturbed Hartree-Fock and Kohn-Sham results employing four-center ERIs. The comparison of SC-ADPT hybrid functional polarizabilities with coupled cluster reference calculations yield semiquantitative agreement. The presented systematic study of the dynamic polarizabilities of oligothiophenes shows that hybrid functionals can overcome the pathological misplacement of excitation poles by the local density and generalized gradient approximations. Good agreement with experimental dynamic polarizabilities for all studied oligothiophenes is achieved with range-separated hybrid functionals in the framework of SC-ADPT.

Asmic: An Exceptional Building Block for Isocyanide Alkylations.

Asmic addresses the long-standing challenge of alkylating isocyanides, providing access to isocyanides with diverse substitution patterns. The o-anisylsulfanyl group serves a critical dual role by facilitating deprotonation-alkylation and providing a latent nucleophilic site through an unusual arylsulfanyl-lithium exchange.

Copper Coordination Features of Human Islet Amyloid Polypeptide: The Type 2 Diabetes Peptide.

Human islet amyloid polypeptide (hIAPP) is the major component of amyloid deposits found in pancreatic ß-cells of patients with type 2 diabetes (T2D). Copper ions have an inhibitory effect on the amyloid aggregation of hIAPP, and they may play a role in the etiology of T2D. However, deeper knowledge of the structural details of the copper-hIAPP interaction is required to understand the molecular mechanisms involved. Here, we performed a spectroscopic study of Cu(II) binding to hIAPP and several variants, using electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), electronic absorption, and circular dichroism (CD) in the UV-vis region in combination with Born-Oppenheimer molecular dynamics (BOMD) and density functional theory geometry optimizations. We find that Cu(II) binds to the imidazole N1 of His18, the deprotonated amides of Ser19 and Ser20, and an oxygen-based ligand provided by Ser20, either via its hydroxyl group or its backbone carbonyl, while Asn22 might also play a role as an axial ligand. Ser20 plays a crucial role in stabilizing Cu(II) coordination toward the C-terminal, providing a potential link between the S20G mutation associated with early onset of T2D, its impact in Cu binding properties, and hIAPP amyloid aggregation. Our study defines the nature of the coordination environment in the Cu(II)-hIAPP complex, revealing that the amino acid residues involved in metal ion binding are also key residues for the formation of ß-sheet structures and amyloid fibrils. Cu(II) binding to hIAPP may lead to the coexistence of more than one coordination mode, which in turn could favor different sets of Cu-induced conformational ensembles. Cu-induced hIAPP conformers would display a higher energetic barrier to form amyloid fibrils, hence explaining the inhibitory effect of Cu ions in hIAPP aggregation. Overall, this study provides further structural insights into the bioinorganic chemistry of T2D.

Improved constraint satisfaction in a simple generalized gradient approximation exchange functional.

Though there is fevered effort on orbital-dependent approximate exchange-correlation functionals, generalized gradient approximations, especially the Perdew-Burke-Ernzerhof (PBE) form, remain the overwhelming choice in calculations. A simple generalized gradient approximation (GGA) exchange functional [A. Vela, V. Medel, and S. B. Trickey, J. Chem. Phys. 130, 244103 (2009)] was developed that improves substantially over PBE in energetics (on a typical test set) while being almost as simple in form. The improvement came from constraining the exchange enhancement factor to be below the Lieb-Oxford bound for all but one value of the exchange dimensionless gradient, s, and to go to the uniform electron gas limit at both s = 0 and s → ∞. Here we discuss the issue of asymptotic constraints for GGAs and show that imposition of the large s constraint, lim(s→∞)s(1/2)F(xc)(n,s)<∞, where F(xc)(n, s) is the enhancement factor and n is the electron density, upon the Vela-Medel-Trickey (VMT) exchange functional yields modest further improvement. The resulting exchange functional, denoted VT{8,4}, is only slightly more complicated than VMT and easy to program. Additional improvement is obtained by combining VT{8,4} or VMT exchange with the Lee-Yang-Parr correlation functional. Extensive computational results on several datasets are provided as verification of the overall performance gains of both versions.

Non-empirical improvement of PBE and its hybrid PBE0 for general description of molecular properties.

Imposition of the constraint that, for the hydrogen atom, the exchange energy cancels the Coulomb repulsion energy yields a non-empirical re-parameterization of the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) exchange-correlation energy functional, and of the related PBE hybrid (PBE0). The re-parameterization, which leads to an increase of the gradient contribution to the exchange energy with respect to the original PBE functional, is tested through the calculation of heats of formation, ionization potentials, electron affinities, proton affinities, binding energies of weakly interacting systems, barrier heights for hydrogen and non-hydrogen transfer reactions, bond distances, and harmonic frequencies, for some well known test sets designed to validate energy functionals. The results for the re-parameterized PBE GGA, called PBEmol, give substantial improvement over the original PBE in the prediction of the heats of formation, while retaining the quality of the original PBE functional for description of all the other properties considered. The results for the hybrids indicate that, although the PBE0 functional provides a rather good description of these properties, the predictions of the re-parameterized functional, called PBEmolß0, are, except in the case of the ionization potentials, modestly better. Also, the results for PBEmolß0 are comparable to those of B3LYP. In particular, the mean absolute error for the bond distance test set is 17% lower than the corresponding error for B3LYP. The re-parameterization for the pure GGA (PBEmol) differs from that for the hybrid (PBEmolß0), illustrating that improvement at the GGA level of complexity does not necessarily provide the best GGA for use in a hybrid.

A MinMax self-consistent-field approach for auxiliary density functional theory.

A MinMax self-consistent-field (SCF) approach is derived in the framework of auxiliary density functional theory. It is shown that the SCF convergence can be guided by the fitting coefficients that arise from the variational fitting of the Coulomb potential. An in-core direct inversion of the iterative subspace (DIIS) algorithm is presented. Due to its reduced memory demand this new in-core DIIS method can be applied without overhead to very large systems with tens of thousands of basis and auxiliary functions. Due to the new DIIS error definition systems with fractional occupation numbers can be treated, too.

A hierarchical transition state search algorithm.

A hierarchical transition state search algorithm is developed and its implementation in the density functional theory program deMon2k is described. This search algorithm combines the double ended saddle interpolation method with local uphill trust region optimization. A new formalism for the incorporation of the distance constrain in the saddle interpolation method is derived. The similarities between the constrained optimizations in the local trust region method and the saddle interpolation are highlighted. The saddle interpolation and local uphill trust region optimizations are validated on a test set of 28 representative reactions. The hierarchical transition state search algorithm is applied to an intramolecular Diels-Alder reaction with several internal rotors, which makes automatic transition state search rather challenging. The obtained reaction mechanism is discussed in the context of the experimentally observed product distribution.

Calculation of exchange-correlation potentials with auxiliary function densities.

The use of Hermite Gaussian auxiliary function densities from the variational fitting of the Coulomb potential for the calculation of exchange-correlation potentials is discussed. The basic working equations for the energy and gradient calculation are derived. The accuracy of this approximation for optimized structure parameters and bond energies are analyzed. It is shown that the quality of the approximation can be systematically improved by enlarging the auxiliary function set. Average errors of 0.5 kcal/mol are obtained with auxiliary function sets including f and g functions. The timings for a series of alkenes demonstrate a substantial performance improvement.