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The previously developed combined Quantum Monte Carlo-Effective Fragment Molecular Orbital (QMC-EFMO) method is extended to systems in which the fragmentation process cuts across covalent molecular bonds.
Preprint of manuscript describing database & physical properties of correlated electron molecular orbital materials.
The implementation of fast relativistic methods based on density functional theory, in conjunction with localized molecular orbital (LMO) based analysis, allows straightforward interpretations of NMR parameters in terms of contributions from core shells, lone pairs, and bonds, for compounds containing elements from across the periodic table. We present a conceptual review of a frequently used LMO analysis of NMR parameters calculated in the presence of spin-orbit interactions and other relativistic effects. An accompanying example focuses on the 15 N shielding in a heavy metal complex.
Low-cost, non-empirical corrections to semi-local density functional theory are essential for accurately modeling transition-metal chemistry. Here, we demonstrate the judiciously modified density functional theory (jmDFT) approach with non-empirical U and J parameters obtained directly from frontier orbital energetics on a series of transition-metal complexes. We curate a set of nine representative Ti(III) and V(IV) d 1 transition-metal complexes and evaluate their flat-plane errors along the fractional spin and charge lines. We demonstrate that while jmDFT improves upon both DFT+U and semi-local DFT with the standard atomic orbital projectors (AOPs), it does so inefficiently. We rationalize these inefficiencies by quantifying hybridization in the relevant frontier orbitals. To overcome these limitations, we introduce a procedure for computing a molecular orbital projector (MOP) basis for use with jmDFT. We demonstrate this single set of d 1 MOPs to be suitable for nearly eliminating all energetic delocalization and static correlation errors. In all cases, MOP jmDFT outperforms AOP jmDFT, and it eliminates most flat-plane errors at non-empirical values. Unlike DFT+U or hybrid functionals, jmDFT nearly eliminates energetic delocalization and static correlation errors within a non-empirical framework.
Strained ring systems play an important role in synthesis and can be characterized by the ring strain energy (RSE). The RSE of 3, 4, 5, and 6 membered saturated and unsaturated ring systems containing N, O, P, and S heteroatoms and H, F, SiMe 3 , and SO 2 Me substituents were calculated at the G3(MP2) composite correlated molecular orbital theory level using up to 5 models to predict the RSE. Generally, the RSE decreased as ring size increased with a substantial decrease from 4 to 5 membered rings. Replacement of a ring CH 2 with P or S reduced the RSE, consistent with less angle strain. The RSE for unsaturated systems were generally greater than for saturated systems due to increased angle strain. No general trends were found with respect to substituent effects. In conclusion, the RSE values suggest that 3-pyrroline and 2-pyrroline and their derivatives may be able to support ring opening metathesis polymerization and warrant further study.
The initial detections of IR vibration-rotation bands in polyatomic molecular ions by recent spectroscopic advances were guided by ab initio prediction of vibrational frequencies. The present calculations predict the vibrational frequencies of additional ions which are candidates for laboratory analysis. Neutral molecule vibrational frequencies were computed at three levels of theory and then compared with experimental data; the effect of scaling was also investigated, in order to determine how accurately vibrational frequencies could be predicted. For 92 percent of the frequencies examined, the relatively simple HF/6-31G theory's vibrational frequencies were within 100/cm of experimental values, with a mean absolute error of 49/cm. On this basis, the frequencies of 30 molecular ions (many possessing astrophysical significance) were computed.
Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.
We introduce a novel machine learning strategy, kernel addition Gaussian process regression (KA-GPR), in molecular-orbital-based machine learning (MOB-ML) to learn the total correlation energies of general electronic structure theories for closed- and open-shell systems by introducing a machine learning strategy. The learning efficiency of MOB-ML(KA-GPR) is the same as the original MOB-ML method for the smallest criegee molecule, which is a closed-shell molecule with multi-reference characters. In addition, the prediction accuracies of different small free radicals could reach the chemical accuracy of 1 kcal/mol by training on one example structure. Accurate potential energy surfaces for the H10 chain (closed-shell) and water OH bond dissociation (open-shell) could also be generated by MOB-ML(KA-GPR). To explore the breadth of chemical systems that KA-GPR can describe, we further apply MOB-ML to accurately predict the large benchmark datasets for closed- (QM9, QM7b-T, and GDB-13-T) and open-shell (QMSpin) molecules.
Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.
The discovery of cyclopropenylidene in space suggests that other C3H2 isomers may be present, and a tentative detection of one such isomer, propargylene (HCCCH), has been reported. Ab initio molecular orbital theory has been used to characterize five low-lying, metastable isomers of cyclopropenylidene. Extended calculations including the electron correlation energy, show that the lowest in energy is singlet propadienylidene, followed by propargylene; the singlet and triplet of the latter are too close in energy to allow an assignment of the ground state; triplet propadienylidene is at a significantly higher energy. Rotational frequencies computed to an expected accuracy of + or - 1 -2 percent do not confirm the tentative detection of propargylene in space, although the discrepancy between theory and the observation is not so great as to unequivocally rule out this possibility.
A virtual reality (VR) session was introduced to an Advanced Inorganic Chemistry class, a class open to junior and senior undergraduate students at University of California, Los Angeles. The VR session helped the students to learn complicated aspects of metal coordination chemistry and molecular orbitals via a three-dimension, immersed experience.
Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.
Two-dimensional covalent organic frameworks (2D-COFs), also referred to as 2D polymer networks, display unusual electronic-structure characteristics, which can significantly enrich and broaden the fields of electronics and spintronics. In this Focus article, the objective of this report is to lay the groundwork for the conceptual description of the fundamental relationships among the COF electronic structures, the symmetries of their 2D lattices, and the frontier molecular orbitals (MOs) of their core and linker components. We focus on monolayers of hexagonal COFs and use tight-binding model analyses to highlight the critical role of the frontier-MO symmetry, in addition to lattice symmetry, in determining the nature of the electronic bands near the Fermi level. We rationalize the intriguing feature that, when the core unit has degenerate highest occupied MOs [or lowest unoccupied MOs], the COF highest valence band [or lowest conduction band] is flat but degenerate with a dispersive band at a high-symmetry point of the Brillouin zone; the consequences of having such band characteristics are briefly described. Multi-layer and bulk 2D COFs are found to maintain the salient features of the monolayer electronic structures albeit with a reduced bandgap due to the interlayer coupling. This Focus article is thus meant to provide an effective framework for the engineering of flat and Dirac bands in 2D polymer networks.
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. The examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.
Dexter energy transfer (DET), also known as spin forbidden energy transfer (e.g., 3 D 1 A → 1 D 3 A), is undergoing renewed interest because of its utility in energy science, photocatalysis, and biomedical imaging. The DET reactions enable exciton fission and fusion and have been recently used to facilitate nanoscale imaging of protein assemblies on cell surfaces. While DET and Förster energy transfer rates are often well described using Fermi’s golden rule, the donor–acceptor couplings for DET may be bridge-state-mediated and depend on the electronic structure of and interactions among the donor, bridge, and acceptor. We provide a simple approach to approximate DET couplings using a product of molecular orbital overlap factors. This approach may be used to guide the design of DET systems with targeted energy-transfer kinetics.
The chemical mechanisms for sulfate formation from sodium chloride and sulfur trioxide, which is a product of jet fuel combustion was determined. Molten sodium sulfate leads to hot corrosion of the protective oxide layers on turbine blades. How yttrium dopants in nidkel-aluminum alloys used in turbine blades reduce the spalling rate of protective alumina films and enhance their adhesion was also determined. Two other fulfate mechanisms were deduced and structure of carbon monoxide on a clean chronium and clean platinum-titanium alloys surfaces was determined. All studies were by use of the atom superposition and electron delocalization molecular orbital (ASED-MO) theory. Seven studies were completed. Their titles and abstracts are given.
Lytic polysaccharide monooxygenases (LPMOs) catalyze the degradation of recalcitrant carbohydrate polysaccharide substrates. These enzymes are characterized by a mononuclear Cu(I) active site with a three-coordinate T-shaped “His-brace” configuration including the N-terminal histidine and its amine group as ligands. Here, this study explicitly investigates the electronic structure of the d 10 Cu(I) active site in a LPMO using Kβ X-ray emission spectroscopy (XES). The lack of inversion symmetry in the His-brace site enables the 3d/p mixing required for intensity in the Kβ valence-to-core (VtC) XES spectrum of Cu(I)-LPMO. These Kβ XES data are correlated to density functional theory (DFT) calculations to define the bonding, and in particular, the frontier molecular orbital (FMO) of the Cu(I) site. These experimentally validated DFT calculations are used to evaluate the reaction coordinate for homolytic cleavage of the H 2 O 2 O–O bond and understand the contribution of this FMO to the low barrier of this reaction and how the geometric and electronic structure of the Cu(I)-LPMO site is activated for rapid reactivity with H 2 O 2 .
Nickel K- and L 2,3 -edge X-ray absorption spectra (XAS) are discussed for 16 complexes and complex ions with nickel centers spanning a range of formal oxidation states from II to IV. K-edge XAS alone is shown to be an ambiguous metric of physical oxidation state for these Ni complexes. Meanwhile, L 2,3 -edge XAS reveals that the physical d-counts of the formally Ni IV compounds measured lie well above the d 6 count implied by the oxidation state formalism. The generality of this phenomenon is explored computationally by scrutinizing 8 additional complexes. The extreme case of NiF 6 2- is considered using high-level molecular orbital approaches as well as advanced valence bond methods. The emergent electronic structure picture reveals that even highly electronegative F-donors are incapable of supporting a physical d 6 Ni IV center. The reactivity of Ni IV complexes is then discussed, highlighting the dominant role of the ligands in this chemistry over that of the metal centers.