Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Can We Safely Obtain Formal Oxidation States from Centroids of Localized Orbitals?

ABSTRACT: The use of centroids of localized orbitals as a method to derive oxidation states (OS) from first-principles is critically analyzed. We explore the performance of the closest-atom distance criterion to assign electrons for a number of challenging systems, including high-valent transition metal compounds, ?-adducts, and transition metal (TM) carbenes. Here, we also introduce a mixed approach that combines the position of the centroids with Bader's atomic basins as an alternative criterion for electron assignment. The closest-atom criterion performs reasonably well for the challenging systems, but wrongly considers O-H and N-H bonds as hydrides. The new criterion fixes this problem, but underperforms in the case of TM carbenes. Moreover, the OS assignment in dubious cases exhibit undesirable dependence on the particular choice for orbital localization.

SUBMITTER: Gimferrer M

PROVIDER: S-EPMC6983110 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Can We Safely Obtain Formal Oxidation States from Centroids of Localized Orbitals?

Gimferrer Martí M Comas-Vilà Gerard G Salvador Pedro P

Molecules (Basel, Switzerland) 20200106 1

The use of centroids of localized orbitals as a method to derive oxidation states (OS) from first-principles is critically analyzed. We explore the performance of the closest-atom distance criterion to assign electrons for a number of challenging systems, including high-valent transition metal compounds, π-adducts, and transition metal (TM) carbenes. Here, we also introduce a mixed approach that combines the position of the centroids with Bader's atomic basins as an alternative criterion for ele ...[more]

PMID: 31935971

Similar Datasets

Fragment Localized Molecular Orbitals.

Project description:We introduce the concept of fragment localized molecular orbitals (FLMOs), which are Hartree-Fock molecular orbitals localized in specific fragments constituting a molecular system. In physical terms, we minimize the local electronic energies of the different fragments, at the cost of maximizing the repulsion between them. To showcase the approach, we rationalize the main interactions occurring in large biological systems in terms of interactions between the fragments of the system. In particular, we study an anticancer drug intercalated within DNA and retinal in anabaena sensory rhodopsin as prototypes of molecular systems embedded in biological matrixes. Finally, the FLMOs are exploited to rationalize the formation of two oligomers, prototypes of amyloid diseases, such as Parkinson and Alzheimer.

| S-EPMC9367013 | biostudies-literature

Initial Maximum Overlap Method Embedded with Extremely Localized Molecular Orbitals for Core-Ionized States of Large Systems.

Project description:Despite great advances in X-ray absorption spectroscopy for the investigation of small molecule electronic structure, the application to biosystems of experimental techniques developed within this research field remains a challenge. To partially circumvent the problem, users resort to theoretical methods to interpret or predict the X-ray absorption spectra of large molecules. To accomplish this task, only low-cost computational strategies can be exploited. For this reason, some of them are single Slater determinant wavefunction approaches coupled with multiscale embedding techniques designed to treat large systems of biological interest. Therefore, in this work, we propose to apply the recently developed IMOM/ELMO embedding method to the determination of core-ionized states. The IMOM/ELMO technique resulted from the combination of the single Slater determinant Δself-consistent-field-initial maximum overlap approach (ΔSCF-IMOM) with the QM/ELMO (quantum mechanics/extremely localized molecular orbital) embedding strategy, a method where only the chemically relevant region of the examined system is treated at fully quantum chemical level, while the rest is described through transferred and frozen extremely localized molecular orbitals (ELMOs). The IMOM/ELMO technique was initially validated by computing core-ionization energies for small molecules, and it was afterwards exploited to study larger biosystems. The obtained results are in line with those reported in previous studies that applied alternative ΔSCF approaches. This makes us envisage a possible future application of the proposed method to the interpretation of X-ray absorption spectra of large molecules.

| S-EPMC9822432 | biostudies-literature

Regularized Localized Molecular Orbitals in a Divide-and-Conquer Approach for Linear Scaling Calculations.

Project description:Non-orthogonal localized molecular orbitals (NOLMOs) have been employed as building blocks for the divide-and-conquer (DC) linear scaling method. The NOLMOs are calculated from subsystems and used for constructing the density matrix (DM) of the entire system, instead of the subsystem DM in the original DC approach. Also, unlike the original DC method, the inverse electronic temperature parameter β is not needed anymore. Furthermore, a new regularized localization approach for NOLMOs has been developed, in which the localization cost function is a sum of the spatial spread function, as in the Boys method, and the kinetic energy, as a regularization measure to limit the oscillation of the NOLMOs. The optimal weight of the kinetic energy can be determined by optimization with analytical gradients. The resulting regularized NOLMOs have enhanced smoothness and better transferability because of reduced kinetic energies. Compared with the original DC, while NOLMO-DC has a similar computational linear scaling cost, the accuracy of NOLMO-DC is better by several orders of magnitude for large conjugated systems and by about 1 order of magnitude for other systems. The NOLMO-DC method is thus a promising development of the DC approach for linear scaling calculations.

| S-EPMC9972215 | biostudies-literature

Design principle for increasing charge mobility of ?-conjugated polymers using regularly localized molecular orbitals.

Project description:The feasibility of using ?-conjugated polymers as next-generation electronic materials is extensively studied; however, their charge mobilities are lower than those of inorganic materials. Here we demonstrate a new design principle for increasing the intramolecular charge mobility of ?-conjugated polymers by covering the ?-conjugated chain with macrocycles and regularly localizing ?-molecular orbitals to realize an ideal orbital alignment for charge hopping. Based on theoretical predictions, insulated wires containing meta-junctioned poly(phenylene-ethynylene) as the backbone units were designed and synthesized. The zigzag wires exhibited higher intramolecular charge mobility than the corresponding linear wires. When the length of the linear region of the zigzag wires was increased to 10 phenylene-ethynylene units, the intramolecular charge mobility increased to 8.5 cm(2) V(-1) s(-1). Theoretical analysis confirmed that this design principle is suitable for obtaining ideal charge mobilities in ?-conjugated polymer chains and that it provides the most effective pathways for inter-site hopping processes.

| S-EPMC3644079 | biostudies-other

Unraveling substituent effects on frontier orbitals of conjugated molecules using an absolutely localized molecular orbital based analysis.

Project description:It is common to introduce electron-donating or electron-withdrawing substituent groups into functional conjugated molecules (such as dyes) to tune their electronic structure properties (such as frontier orbital energy levels) and photophysical properties (such as absorption and emission wavelengths). However, there lacks a generally applicable tool that can unravel the underlying interactions between orbitals from a substrate molecule and those from its substituents in modern electronic structure calculations, despite the long history of qualitative molecular orbital theory. In this work, the absolutely localized molecular orbitals (ALMO) based analysis is extended to analyze the effects of substituent groups on the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of a given system. This provides a bottom-up avenue towards quantification of effects from distinct physical origins (e.g. permanent electrostatics/Pauli repulsion, mutual polarization, inter-fragment orbital mixing). For the example case of prodan (a typical dye molecule), it is found that inter-fragment orbital mixing plays a key role in narrowing the HOMO-LUMO gap of the naphthalene core. Specifically, an out-of-phase mixing of high-lying occupied orbitals on the naphthalene core and the dimethylamino group leads to an elevated HOMO, whereas an in-phase combination of LUMOs on the naphthalene core and the propionyl group lowers the LUMO energy of the entire molecule. We expect this ALMO-based analysis to bridge the gap between concepts from qualitative orbital interaction analysis and quantitative electronic structure calculations.

| S-EPMC6253684 | biostudies-literature

ℤ-Classified Topological Phases and Bound States in the Continuum Induced by Multiple Orbitals.

Project description:ℤ-classified higher-order topological insulators (HOTIs) with chiral-symmetric higher-order topological phases protected by multipole chiral numbers (MCNs) have attracted extensive interest recently. However, how to design artificial ℤ-classified HOTIs with multiple topological phases remains an unresolved issue. Here, multiorbital degrees of freedom are introduced to acoustic crystals and the various methods of topological phase transitions are achieved for the orbital ℤ-classified HOTIs. Experimental results demonstrate the realization the coexistence of corner modes with distinct mechanisms within one single model. This provides a pathway for finding ℤ-classified with large MCNs independent of long-range coupling. Additionally, a universal approach is introduced here to fabricate topological bound states in the continuum derived from the discrepant onsite energy of degenerate p-orbitals. These findings provide new insights into the study of topological wave physics using orbital degrees of freedom and may pave the way for designing innovative orbital topological devices for sensing and computing.

| S-EPMC11905062 | biostudies-literature

Nearest shrunken centroids via alternative genewise shrinkages.

Project description:Nearest shrunken centroids (NSC) is a popular classification method for microarray data. NSC calculates centroids for each class and "shrinks" the centroids toward 0 using soft thresholding. Future observations are then assigned to the class with the minimum distance between the observation and the (shrunken) centroid. Under certain conditions the soft shrinkage used by NSC is equivalent to a LASSO penalty. However, this penalty can produce biased estimates when the true coefficients are large. In addition, NSC ignores the fact that multiple measures of the same gene are likely to be related to one another. We consider several alternative genewise shrinkage methods to address the aforementioned shortcomings of NSC. Three alternative penalties were considered: the smoothly clipped absolute deviation (SCAD), the adaptive LASSO (ADA), and the minimax concave penalty (MCP). We also showed that NSC can be performed in a genewise manner. Classification methods were derived for each alternative shrinkage method or alternative genewise penalty, and the performance of each new classification method was compared with that of conventional NSC on several simulated and real microarray data sets. Moreover, we applied the geometric mean approach for the alternative penalty functions. In general the alternative (genewise) penalties required fewer genes than NSC. The geometric mean of the class-specific prediction accuracies was improved, as well as the overall predictive accuracy in some cases. These results indicate that these alternative penalties should be considered when using NSC.

| S-EPMC5310887 | biostudies-literature

Compact localized states in magnonic Lieb lattices.

Project description:Lieb lattice is one of the simplest bipartite lattices, where compact localized states (CLS) are observed. This type of localization is induced by the peculiar topology of the unit cell, where the modes are localized only on selected sublattices due to the destructive interference of partial waves. We demonstrate the possibility of magnonic Lieb lattice realization, where flat bands and CLS can be observed in the planar structure of sub-micron in-plane sizes. Using forward volume configuration, the Ga-doped YIG layer with cylindrical inclusions (without Ga content) arranged in a Lieb lattice with 250 nm period was investigated numerically (finite-element method). The structure was tailored to observe, for a lowest magnonic bands, the oscillatory and evanescent spin waves in inclusions and matrix, respectively. Such a design reproduces the Lieb lattice of nodes (inclusions) coupled to each other by the matrix with the CLS in flat bands.

| S-EPMC10403553 | biostudies-literature

An examination of the nature of localized molecular orbitals and their value in understanding various phenomena that occur in organic chemistry.

Project description:While canonical molecular orbitals have been used in computational chemistry for almost a century, the use of localized molecular orbitals is relatively new, and generating them has been difficult until recently. This has impeded their routine use in modeling chemical systems and reactions so that, even though localized molecular orbitals can now be generated easily, their usefulness in interpreting chemical phenomena has not been properly appreciated. Localized molecular orbitals can provide useful insights into chemical phenomena such as two-electron bonds, π delocalization, and lone pairs. A potentially important application would be interpreting the phenomena that occur in chemical reactions, in particular those reactions which can be described using the Lewis curly-arrow electron pushing convention. This paper considers how canonical and localized molecular orbitals are generated, their usefulness and limitations, and some issues that could be considered controversial regarding their nature, and it presents examples of the usefulness of LMOs in describing six chemical systems and one reaction.

| S-EPMC6306422 | biostudies-literature