Core Potentials Research Articles

Comprehensive Benchmark Study on the Calculation of 29Si NMR Chemical Shifts

A comprehensive and diverse benchmark set for the calculation of 29Si NMR chemical shifts is presented. The SiS146 set includes 100 silicon containing compounds with 146 experimentally determined reference 29Si NMR chemical shifts measured in nine different solvents in a range from -400 to +828 ppm. Silicon atoms bound to main group elements as well as transition metals with coordination numbers of 2-6 in various bonding patterns including multiple bonds and coordinative and aromatic bonding are represented. The performance of various common and specialized density functional approximations including (meta-)GGA, hybrid, and double-hybrid functionals in combination with different AO basis sets and for differently optimized geometries is evaluated. The role of scalar-relativistic effects is further investigated by inclusion of the zeroth order regular approximation (ZORA) method into the calculations. GGA density functional approximations (DFAs) are found to outperform hybrid DFAs with B97-D3 performing best with an MAD of 7.2 ppm for the subset including only light atoms (Z < 18), while TPSSh is the best tested hybrid functional with an MAD of 10.3 ppm. For 29Si cores in the vicinity of heavier atoms, the application of ZORA proved indispensable. Inclusion of spin-orbit effects into the 29Si NMR chemical shift calculation decreases the mean absolute deviations by up to 74% compared to calculations applying effective core potentials.

Structure of lanthanide nitrates in solution and in the solid state: DFT modelling of hydration effects

Five types of [Ln(NO3)3(H2O)4] neutral complexes with different mutual arrangement of nitrato and aqua ligands are established by the analysis of crystallographic data. Quantum chemical calculations performed at the level of density functional theory employing full-electron relativistic approach and effective core potential with different functionals and basis sets demonstrate that each of these structure types converges to a specific energy minimum, thus these types should be considered as isomers. Besides this, two isomers have been found for [Ln(NO3)3(H2O)3] complexes. In all structures of isomers optimized with the gas-phase approximation, Ln–ONO2 bonds are significantly shorter that Ln–OH2 bonds, in contrast to the results of X-ray diffraction and EXAFS studies of single crystals and aqueous solutions, respectively. This discrepancy arises from the fact that in crystals and solutions, complex molecules form numerous hydrogen bonds, which enhance charge transfer in the H2O → Ln3+ → NO3− chains and increase the relative stability of isomers where the nitrate anions are arranged separately from the aqua ligands. The effect of environment on electronic and spatial structures of [Ln(NO3)3(H2O)n] (n = 3, 4) complexes has been modelled at the levels of polarizable continuum model (PCM) and cluster approach. When using PCM, the similarity of quantum chemical and experimental bond lengths enhances, but complete agreement is not reached. Better agreement is achieved within the clusters {[La(NO3)3(H2O)4]∙nH2O} (n = 18, 21, 32, 50), where the effects of hydrogen bonding are modelled explicitly. These clusters are highly flexible with both hydration shells and the central core being easily rearranged under the effect of outer water molecules. With an increase in cluster size, new local energy minima appear related with the structures with monodentate nitrate anion and with nitrate anion positioned in the second coordination sphere of the cation. Joint analysis of simulation results together with literature data on the structure and dynamic behavior of lanthanide nitrates in aqueous solutions allows conclusion that the entire set of equilibria involving [La(NO3)3(H2O)n] complexes should be considered as a dynamic combinatorial library.

Removing artifacts in polarizable embedding calculations of one- and two-photon absorption spectra of fluorescent proteins.

The multiscale calculations involving excited states may suffer from the electron spill-out (ESO) problem. This seems to be especially the case when the environment of the core region, described with the electronic structure method, is approximated by a polarizable force field. The ESO effect often leads to incorrect physical character of electronic excitations, spreading outside the quantum region, which, in turn, results in erroneous absorption spectra. In this work, we investigate means to remove the artifacts in one-photon absorption (OPA) and two-photon absorption (TPA) spectra of green and yellow fluorescent protein representatives. This includes (i) using different basis sets, (ii) extending the core subsystem beyond the chromophore, (iii) modification of polarization interaction between the core region and its environment, and (iv) including the Pauli repulsion through effective core potentials (ECPs). Our results clearly show that ESO is observed when diffuse functions are used to assemble the multielectron wave function regardless of the exchange-correlation functional used. Furthermore, extending the core region, thus accounting for exchange interactions between the chromophore and its environment, leads to even more spurious excited states. Also, damping the interactions between the core subsystem and the polarizable force field is hardly helpful. In contrast, placing ECPs in the position of sites creating the embedding potential leads to the removal of artificious excited states that presumably should not be observed in the OPA and TPA spectra. We prove that it is a reliable and cost-effective approach for systems where the covalent bond(s) between the core region and its environment must be cut.

Structure, reactions, and electronic spectra of the rare gas cyanohydrides and isocyanohydrides, HRgCN and HRgNC (Rg = Xe or Rn)

The low-energy electronic excitations of HRgCN and HRgNC (Rg = Xe, Rn) were computed at the TDDFT level of theory, both in the gas phase and in xenon cluster. It was found that the most prominent peak in the spectra was due to the highest occupied molecular orbital (HOMO) to lowest unoccupied molecular orbital (LUMO) transition (∼6 eV for HRgCN and ∼4.5 eV for HRgNC). Cluster confinement brought about bathochromic shifts in the spectra and better agreement with experiment for HXeCN. The effects of spin–orbit coupling (SOC) in the heavier Rn systems were investigated: for HRnCN, SOC red-shifted the HOMO–LUMO peak, while it blue-shifted the HOMO–LUMO peak for HRnNC. Geometry optimizations were carried out for the HRgCN and HRgNC systems to locate minima and transition states for dissociation and isomerization. Effects of isotopic substitution on reaction rates were predicted. A new model core potentials basis set was introduced and effectiveness of several pseudopotential basis sets was studied.

Markovnikov versus anti‐Markovnikov addition and C–H activation: Pd–Cu synergistic catalysis

Copper‐ and palladium‐mediated transmetalation and coupling reactions are the backbone to several synthetic methodologies in organic chemistry for C–C bond formation. Computer‐aided simulations using density functional theory (DFT) (B3LYP‐D3 functional with 6‐31G** and effective core potential (ECP)‐LACVP** for heavy atoms for optimizations and cc‐pVTZ(−f) and ECP‐LACV3P** for single‐point calculations) was used to shed light on the probable mechanism of a novel synergistic Cu/Pd catalysts for the coupling of alkene, (Bpin)2 (where, pin = pinacolate), and vinyl‐ or aryl‐halogenated analogues. Every single conceivable pathway was carefully contemplated, and the base minimum energy pathway was found effectively. The copper‐catalyzed nucleophilic generation yields anti‐Markovnikov product using styrene as an alkene. This study affirms quantitatively and accurately how the reaction proceeds and at which steps of the synergistic catalysis the demand of the transmetalation and nucleophile formation for the C–C coupling using phosphine ligands arise. We conclude that the E and Z selectivity depends on the stereochemistry of the substrates used.

Binding and excitations in SixHy molecular systems using quantum Monte Carlo.

We present high-accuracy correlated calculations of small SixHy molecular systems in both the ground and excited states. We employ quantum Monte Carlo (QMC) together with a variety of many-body wave function approaches based on basis set expansions. The calculations are carried out in a valence-only framework using recently derived correlation consistent effective core potentials. Our primary goal is to understand the fixed-node diffusion QMC errors in both the ground and excited states with single-reference trial wave functions. Using a combination of methods, we demonstrate the very high accuracy of the QMC atomization energies being within ≈0.07 eV or better when compared with essentially exact results. By employing proper choices for trial wave functions, we have found that the fixed-node QMC biases for total energies are remarkably uniform ranging between 1% and 3.5% with absolute values at most ≈0.2 eV across the systems and several types of excitations such as singlets and triplets as well as low-lying and Rydberg-like states. Our results further corroborate that Si systems, and presumably also related main group IV and V elements of the periodic table (Ge, Sn, etc), exhibit some of the lowest fixed-node biases found in valence-only electronic structure QMC calculations.

The Interaction of Adenine with Zn12O12 Cluster from Density Functional Theory

Geometries associated energy gap and electronic properties of adenine, DNA base interaction on the ZnO model cluster have been investigated by using density functional theory with the B3LYP exchange-correlation potential and effective core potential (ECP) LanL2DZ basis sets. The most stable interaction characteristics were analysed with respect to the binding energy, frontier orbital, elemental positions. Natural population analysis charge is also examined to understand the associated charge transfer in structures of cluster and complex. In the Zn-N bonding, combination coefficient from atom orbitals of nitrogen is much higher than that of zinc. The corresponding weight for this coefficient is 94.80%. The results of this study can serve as an orientation for the design of composite material in biomedical nanotechnology.

Ab initio study of R-dependent behavior of the hyperfine structure parameters for the [formula omitted] states of LiRb and LiCs

Diagonal a3Σ1+-a3Σ1+ and off–diagonal X1Σ0++-a3Σ0-+ magnetic hyperfine structure (HFS) matrix elements were calculated ab initio for the LiRb and LiCs molecules in a wide range of internuclear distances using the multi–reference Fock space coupled clusters method with generalized relativistic effective core potentials to describe the four–component valence wavefunctions near the nuclei. At large distances, both HFS functions vary little, though they may fluctuate by as much as 12 to 24% in the intermediate range. The plateau exhibited by the a3Σ1+-a3Σ1+ HFS function at 4–5 Å, could be attributed to pronounced spin–orbit coupling of the intersecting a3Σ+ and b3Π states.

Hybridizing pseudo-Hamiltonians and non-local pseudopotentials in diffusion Monte Carlo.

An accurate treatment of effective core potentials (ECPs) requires care in continuum quantum Monte Carlo (QMC) methods. While most QMC studies have settled on the use of familiar non-local (NL) pseudopotentials with additional localization approximations, these approaches have been shown to result in moderate residual errors for some classes of molecular and solid state applications. In this work, we revisit an idea proposed early in the history of QMC ECPs that does not require localization approximations, namely, a differential class of potentials referred to as pseudo-Hamiltonians. We propose to hybridize NL potentials and pseudo-Hamiltonians to reduce residual non-locality of existing potentials. We derive an approach to recast pseudopotentials for 3d elements as hybrid pseudo-Hamiltonians with optimally reduced NL energy. We demonstrate the fidelity of the hybrid potentials by studying atomic ionization potentials of Ti and Fe and the binding properties of TiO and FeO molecules with diffusion Monte Carlo (DMC). We show that localization errors have been reduced relative to potentials with the same NL channels for Sc-Zn by considering the DMC energy change with respect to the choice of approximate localization. While localization error decreases proportionate to the reduced NL energy without a Jastrow, with a Jastrow, the degree of reduction decreases at higher filling of the d-shell. Our results suggest that a subset of existing ECPs may be recast in this hybrid form to reduce the DMC localization error. They also point to the prospect of further reducing this error by generating ECPs within this hybrid form from the start.

Tunneling matrix element and tunneling pathways of protein electron transfer calculated with a fragment molecular orbital method

Practical ways to calculate the tunneling matrix elements and analyze the tunneling pathways for protein electron-transfer (ET) reactions with a fragment molecular orbital (FMO) method are presented. The straightforward use of minimal basis sets only for the atoms involved in the covalent bond detachment in FMO can properly describe the ETs through the protein main-chains with the cost-effective two-body corrections (FMO2) without losing the quality of double-zeta basis sets. The current FMO codes have been interfaced with density functional theory, polarizable continuum model, and model core potentials, with which the FMO-based protein ET calculations can consider the effects of electron correlation, solvation, and transition-metal redox centers. The reasonable performance of the FMO-based ET calculations is demonstrated for three different sets of protein-ET model molecules: (1) hole transfer between two tryptophans covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, (2) ET between two plastoquinones covalently bridged by a polyalanine linker in the ideal α-helix and β-strand conformations, and (3) hole transfer between ruthenium (Ru) and copper (Cu) complexes covalently bridged by a stretch of a polyglycine linker as a model for Ru-modified derivatives of azurin.

Assessment of the proposed pseudo-potential theoretical model for the static and dynamic Raman scattering intensities: Multivariate statistical approach to quantum-chemistry protocols.

Accurate calculation of molecular polarizabilities and Raman intensities required high-level correlated wave functions (CCSD) and large basis set with the inclusion of electronic correlation within experimental precision. These requirements, in terms of time and computation, are economically costly. Polarized Gaussian basis sets adapted to effective core potentials (ECPs) for the static and frequency dependent Raman intensities is presented. The results of the proposed basis sets at CCSD and DFT levels in comparison with Sadlej-pVTZ, as reference basis set, show quite a good quantitative agreement in the properties with a valuable reduction in the computational time and resources. Multivariate principal component analysis (PCA) was performed to study the assessment of the efficiency of proposed methodology and diagnose the inherent information related to the kind of normal vibrational mode of each molecule, based on the variations in the computed Raman intensities. The results, in the form of score-plots, explored a clear segregation and classification among the Raman intensities data, revealing its dependence on the excitation frequencies of laser and nature of the vibrational mode of each molecule of interest. Moreover, the projection of the loadings-plots of the PCs successfully enabled to classify the most correlated computational methods in to the same groups, and made isolations of the less efficient basis functions at the corresponding theoretical method.

Inspired by the growth characteristic of leaf epidermis cell walls: A bio-ITCLC core for supporting a flexible skin with combined morphing applications

Inspired by low transverse and high vertical stiffness characteristics of leaf epidermis cell walls, a biomimetic Isosceles Trapezoid Corrugated Lattice Cellular (bio-ITCLC) core is designed and fabricated. The constitutive model of the bio-ITCLC sandwich panel under out-of-plane compression is built to demonstrate great potential of the bio-ITCLC core for decoupling the mutual restriction of small tangential and large normal stiffness of a flexible skin. After that, the variable stiffness, equating to the continually changing stiffness characteristic of epidermis cell walls, is introduced in the above constitutive model to capture the growth behavior of a leaf shape via epidermis cell divisions to study morphing mechanisms of a flexible skin. On this basis, by the supporting effect of self-adaption units in the bio-ITCLC core, with new circumstances, is proposed to be one promising approach for designing a flexible skin with the small tangential and large normal stiffness for multi-morphing applications.

Targeted Theranostic Nano Vehicle Endorsed with Self‐Destruction and Immunostimulatory Features to Circumvent Drug Resistance and Wipe‐Out Tumor Reinitiating Cancer Stem Cells

The downsides of conventional cancer monotherapies are profound and enormously consequential, as drug-resistant cancer cells and cancer stem cells (CSC) are typically not eliminated. Here, a targeted theranostic nano vehicle (TTNV) is designed using manganese-doped mesoporous silica nanoparticle with an ideal surface area and pore volume for co-loading an optimized ratio of antineoplastic doxorubicin and a drug efflux inhibitor tariquidar. This strategically framed TTNV is chemically conjugated with folic acid and hyaluronic acid as a dual-targeting entity to promote folate receptor (FR) mediated cancer cells and CD44 mediated CSC uptake, respectively. Interestingly, surface-enhanced Raman spectroscopy is exploited to evaluate the molecular changes associated with therapeutic progression. Tumor microenvironment selective biodegradation and immunostimulatory potential of the MSN-Mn core are safeguarded with a chitosan coating which modulates the premature cargo release and accords biocompatibility. The superior antitumor response in FR-positive syngeneic and CSC-rich human xenograft murine models is associated with a tumor-targeted biodistribution, favorable pharmacokinetics, and an appealing bioelimination pattern of the TTNV with no palpable signs of toxicity. This dual drug-loaded nano vehicle offers a feasible approach for efficient cancer therapy by on demand cargo release in order to execute complete wipe-out of tumor reinitiating cancer stem cells.

An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling

Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate states are usually created by mixing the energies or parameters of the end states according to a coupling parameter λ. The choice of the procedure has a strong impact on the efficiency of the calculation, as it affects both the encountered energy barriers and the phase space overlap between the states. The present work builds on the connection between the minimum variance pathway (MVP) and enveloping distribution sampling (EDS). It is shown that both methods can be regarded as special cases of a common scheme referred to as λ-EDS, which can also reproduce the behavior of conventional λ-intermediate states. A particularly attractive feature of λ-EDS is its ability to emulate the use of soft core potentials (SCP) while avoiding the associated computational overhead when applying efficient free energy estimators such as the multistate Bennett's acceptance ratio (MBAR). The method is illustrated for both relative and absolute free energy calculations considering five benchmark systems. The first two systems (charge inversion and cavity creation in a dipolar solvent) demonstrate the use of λ-EDS as an alternative coupling scheme in the context of thermodynamic integration (TI). The three other systems (change of bond length, change of dihedral angles, and cavity creation in water) investigate the efficiency and optimal choice of parameters in the context of free energy perturbation (FEP) and Bennett's acceptance ratio (BAR). It is shown that λ-EDS allows larger steps along the alchemical pathway than conventional intermediate states.

Weak bonding of the hydrogen molecule by the S-state lanthanide ions Eu+, Yb+ and Lu+ from ab initio calculations

The complexes formed by the singly-charged S-state lanthanide ions Eu+, Yb+ and Lu+ with the hydrogen molecule are investigated using the ab initio coupled cluster CCSD(T) method with effective core potential and all-electron descriptions of lanthanides. Equilibrium structures, two-dimensional interaction potential energy surfaces and variational energies of the lowest rovibrational energy levels are obtained. Three complexes considered are qualitatively similar and exhibit weak bonding and perturbation of hydrogen fragment, as well as strong vibrational anharmonicity.

Reaction mechanism for hydrogen production using the Pd4 cluster and formic acid by DFT

A systematic study was conducted on the production of hydrogen from formic acid with a Pd4 cluster using density functional theory (DFT) with the B3LYP and the 6-31G** orbital basis set for the C, H and O atoms, while a LANL2DZ effective core potential was used for palladium atoms. The thermodynamic results obtained show a favorable reaction mechanism for producing hydrogen with energy barriers lower than 30 kcal/mol. Moreover, the nature of the bonds involved in all system were analyzed using the theory of atoms in molecules (AIM) identifying the non-covalent interactions in this type of system.

Quebec’s Fracking Restrictions: Squandered Opportunity or Prudent Conservation?

ABSTRACT This article first reviews key developments in the Quebec natural gas fracking timeline from initial exploratory well fracking in 2007 to the 2011 moratorium and the 2018 fracking prohibition. Next, the article estimates potential jobs and wealth losses from the prohibition in Quebec via a comparison between intensive fracking in northeastern Pennsylvania (which is similar in size to Quebec’s core potential fracking region) and adjacent counties in New York state where fracking is prohibited. Quebec’s job loss from fracking prohibition is estimated to be quite modest. Moreover, the estimated wealth effect range shows that allowing development of Quebec’s shale gas reserves may well have led to net wealth losses rather than gains for its citizens because of large declines in natural gas prices. While future shale gas development in Quebec is a possibility, given the preferences of Quebec’s citizens, the weak profitability prospects of the shale gas sector, and the ongoing cost reductions for solar and wind power, it seems most likely that Quebec’s Utica Shale gas reserves will remain undeveloped and that this will be a sound policy decision.

Mapping molecular electrostatic potential (MESP) for fulleropyrrolidine and its derivatives

Mapping molecular electrostatic potential (MESP) maps for chemical structure has become of great concern. Since it may explain valuable information about the interaction, active sites as well as determining the nature of chemical addition, through which a molecule is most probable to undergo; either electrophilic or nucleophilic addition. Calculations at a DFT high theoretical level and MESP maps for fulleropyrrolidine and its derivatives were carried out. The relation between total dipole moment (TDM) and the constructed MESPs were also investigated. Three different series of fulleropyrrolidine derivatives; ortho, meta and para, were presented. Results show that positioning the same element at different sites may change significantly TDM of the structure. The electron density of the fullerene structure appears as a red ellipse shape indicating an extremely negative region that is most likely to undergo nucleophilic reactions. The addition of electronegative substitutes; O and N, creates negative potentials at the terminal of the structure referring that electrophilic reactions are most probable there. The negative potential of fullerene core has the main role in determining the TDM direction.

The Study of a Structural and Electronic Properties of Two-Dimensional Flat Layer Arsenene Using Planewaves Density Functional Calculation

We explore the structural and electronic properties of a single layer arsenene using the state of art, first principle approach from density functional theory (DFT). All the calculation was conducted using an open source DFT code, adopted the planewaves (PWs) method by Quantum Espresso (QE). The calculation utilized an exchange correlation potential of electron parametrized by Perdew-Burke-Ernzerhof (PBE) under generalized gradient approximation (GGA) functional scheme. Meanwhile, the pseudopotential assigned for the core electron is the projector typed augmented-wave with the core potential correction, generated using "atomic" code. All those parameters resulted an optimized structure of the honeycomb arsenene with lattice constant of 4.4971 Ǻ. The arsenene layer occupy a bond length value of 2.5964 Ǻ as measured between its neighbouring bonded atoms. From an optimized structure, we explore its electronic bandstructure plotted from 3 highly symmetries point for 2-dimensional (2D) material known as ‘’, ‘’ and ‘’ with 3 electron pathways. The total number of bands considered in bandstruture plotting is 10, where 5 bands will consider as valance bands while another 5 is conduction bands. The bandstructure shows that a single layer flat arsenene exhibits the characteristics of a conductor due to the overlapping of band near to Fermi level. Dirac cone were also noticed near to the Fermi energy level of the bandstructure. Lastly, we study the total electron density for the whole structure to reveal its bonding characteristics. The contour plot of electron densities between two bounded atoms displayed a pure covalent bond characteristic. The findings of this work is expected to contribute to the key of the electronic devices development, optoelectronics, and sensor devices based on 2D material technology.Keywords: flat layer arsenene, density of state, electron density, electronic band structure

Theoretical determination of half-wave potentials for phenanthroline-, bipyridine-, acetylacetonate-, and glycinate-containing copper (II) complexes.

We report a protocol for the evaluation of theoretical half-wave potential (E1/2) using a set of 22 mixed chelate copper (II) complexes containing 1,10-phenanthroline and 2,2'-bipyridine derivatives as primary ligands, and acetylacetonate or glycinate as secondary ligands (formally from the Casiopeínas® family) for which accurate experimental values were determined in a 2/5 mixture of ethanol/water. We have calibrated the BP86, PBE, PBE0, B3LYP, M06-2X, and ω-B97XD functionals, using the Los Alamos LANL2DZ and Stuttgart-Köln SDDAll effective core potentials for the Cu and Fe atoms and the 6-311+G* basis set for the C, H, O, and N atoms. To address the solvent effects, we have saturated the first solvation shell with up to 9 water molecules for the explicit model and compared it with the Continuum Like-Polarizable Continuum Model (CPCM) implicit solvent scheme. We found that the PBE/LANL2DZ-6-311+G* protocol (with the CPCM implicit solvent scheme with an effective dielectric constant ε = 64.9121 for the 2/5 mixture of ethanol/water) yields the overall best performance. The theoretical values are compared with experimental data, three of which are reported here for the first time. We find good correlations between the theoretical and experimental E1/2 values for the 2,2'-bipyridine derivatives (R2 = 0.987, MAE = 86mV) and 1,10-phenanthroline derivatives (R2 = 0.802, MAE = 58.4mV). The correlation trends have been explained in terms of the copper atom's ability to be reduced in the presence of the ligands. The Gibbs free energy differences at 298K obtained for the redox reactions show that the more flexible secondary ligands (acetylacetonate) lead to larger entropic contributions which, as expected, increase the average MAE values as compared with the more rigid ligands (glycine). The present protocol yields lower MAEs as compared with previous approaches for similar mixed and flexible Cu(II) complexes.