Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fragment Localized Molecular Orbitals.

ABSTRACT: 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.

SUBMITTER: Giovannini T

PROVIDER: S-EPMC9367013 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Fragment Localized Molecular Orbitals.

Giovannini Tommaso T Koch Henrik H

Journal of chemical theory and computation 20220727 8

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 particula ...[more]

PMID: 35895631

Similar Datasets

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

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

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

Energy Ordering of Molecular Orbitals.

Project description:Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations.

| S-EPMC5220489 | biostudies-literature

Magnetic molecular orbitals in MnSi.

Project description:A large body of knowledge about magnetism is attained from models of interacting spins, which usually reside on magnetic ions. Proposals beyond the ionic picture are uncommon and seldom verified by direct observations in conjunction with microscopic theory. Here, using inelastic neutron scattering to study the itinerant near-ferromagnet MnSi, we find that the system's fundamental magnetic units are interconnected, extended molecular orbitals consisting of three Mn atoms each rather than individual Mn atoms. This result is further corroborated by magnetic Wannier orbitals obtained by ab initio calculations. It contrasts the ionic picture with a concrete example and presents an unexplored regime of the spin waves where the wavelength is comparable to the spatial extent of the molecular orbitals. Our discovery brings important insights into not only the magnetism of MnSi but also a broad range of magnetic quantum materials where structural symmetry, electron itinerancy, and correlations act in concert.

| S-EPMC9812394 | biostudies-literature

Toward Polaritonic Molecular Orbitals for Large Molecular Systems.

Project description:A comprehensive understanding of electron-photon correlation is essential for describing the reshaping of molecular orbitals in quantum electrodynamics (QED) environments. The strong coupling QED Hartree-Fock (SC-QED-HF) theory tackles these aspects by providing consistent molecular orbitals in the strong coupling regime. The previous implementation, however, has significant convergence issues that limit the applicability. In this work, we introduce two second-order algorithms that significantly reduce the computational requirements, thereby enhancing the modeling of large molecular systems in QED environments. Furthermore, the implementation will enable the development of correlated methods based on a reliable molecular orbital framework as well as multi-level methodologies able to model the inclusion of solvent effects in this kind of complex systems.

| S-EPMC11500296 | biostudies-literature

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

Project description: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 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.

| S-EPMC6983110 | 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

Exact Analytical Form of Diatomic Molecular Orbitals.

Project description:We provide the exact analytical form of diatomic molecular orbitals, as given by the solutions of a single-electron diatomic molecule with arbitrary nuclear charges, using our recently developed method for solving Schrödinger equations. We claim that the best representation of the wave function is a factorized form including a power prefactor, an exponentially decaying term, a modulator function on the exponential, and additional factors accounting for nodal surfaces and the magnetic quantum number. Applying our method, we have identified unexpected extreme points along the potential energy curves, hence revealing the limitations of the well-known concepts of bonding and antibonding.

| S-EPMC9260940 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data