Topics

Calculation of Free-Energy Barriers with TD-DFT: A Case Study on Excited-State Proton Transfer in Indigo.

08:00 EDT 12th September 2019 | BioPortfolio

Summary of "Calculation of Free-Energy Barriers with TD-DFT: A Case Study on Excited-State Proton Transfer in Indigo."

The performance of time-dependent density functional theory (TD-DFT) for the calculation of excited states of molecular systems has been the subject of many benchmark studies. Often, these studies focus on excitation energies or, more recently, excited-state equilibrium geometries. In this work, we take a different angle by instead exploring how well TD-DFT reproduces experimental free-energy barriers of a well-known photochemical reaction: the excited-state proton transfer (ESPT) in indigo. Specifically, by exploiting the possibility of using TD-DFT to locate and compute free energies of first-order saddle points in excited states, we test the performance of several popular density functionals in reproducing recently determined experimental free-energy barriers for ESPT in indigo and in an -hexyl substituted derivative thereof. Through the calculations, it is found that all of the tested functionals perform quite well, uniformly overestimating the experimental values by 1.4-3.5 (mean error) and 2.5-5.5 kcal mol (maximum error) only. Given that these errors are not larger than those typically observed when barriers for ground-state proton transfer reactions are calculated in ground-state DFT, the results highlight the potential of TD-DFT to enable accurate modeling of ESPT reactions based on free energies and explicit localization of transition states.

Affiliation

Journal Details

This article was published in the following journal.

Name: The journal of physical chemistry. A
ISSN: 1520-5215
Pages:

Links

DeepDyve research library

PubMed Articles [29961 Associated PubMed Articles listed on BioPortfolio]

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.

Binding free energy (Δ) computation can play an important role in prioritizing compounds to be evaluated experimentally on their affinity for target proteins, yet fast and accurate Δ calculation rem...

An explorative study on MurE inhibitor: induced fit docking, binding free energy calculation, and molecular dynamics.

MurE enzyme catalyzes the addition of l-lysine as third residue of the peptidoglycan peptide moiety. Due to the high substrate specificity and its ubiquitous nature among bacteria, MurE enzyme is cons...

Experimental and theoretical investigation on photodegradation mechanisms of naproxen and its photoproducts.

The photochemical degradation of the pharmaceuticals and personal care products (PPCPs) has attracted increasing attention. In this study, a deep inspection of the photolysis mechanisms of naproxen an...

Excited State Potential Energy Surfaces, Conical Intersections and Analytical Gradients from Ground State Density Functional Theory.

Kohn-Sham density functional theory (KS-DFT) has been a well-established theoretical foundation for ground state electronic structure and has achieved great success in practical calculations. Recently...

Engineering Excited-State Interactions at Ultracold Temperatures.

Using a recently developed method for precisely controlling collision energy, we observe a dramatic suppression of inelastic collisions between an atom and ion (Ca+Yb^{+}) at low collision energy. Thi...

Clinical Trials [7601 Associated Clinical Trials listed on BioPortfolio]

Dual Energy CT: A New Method for Better Dose Calculation in Proton Beam Therapy

Researchers want to compare proton stopping ratios, used for proton beam therapy planning, calculated based on single energy CT and dual energy CT images; with the intension of improve upo...

The Effect of Fat Mass, Fat-free Mass and Resting Metabolic Rate on Energy Intake

The present study was based on secondary analysis using the non-intervention control conditions of five separate studies with common measures. The current analysis examine the indirect and...

Case Management in HCV Infected PWID

To study the impact of case management on the outcome of the care of chronic hepatitis C in people who inject drugs (PWID). By creating the function of case manager, the investigators will...

A Case Control Study to Identify the Role of Epigenetic Regulation of Genes Responsible for Energy Metabolism and Mitochondrial Function in the Obesity Paradox in Cardiac Surgery

This is a prospective, single-center case control comparison of expression of target genes responsible for energy utilization, mitochondrial function and oxidative stress and levels of his...

Ramadan and Energy Expenditure Study

Ramadan fasting entails abstinence from eating and drinking between dawn and sunset. During this month major changes in meal times and patterns, sleeping times and activity occur. Starvati...

Medical and Biotech [MESH] Definitions

Calculation of the energy expenditure in the form of heat production of the whole body or individual organs based on respiratory gas exchange.

Electron transfer through the cytochrome system liberating free energy which is transformed into high-energy phosphate bonds.

The study of the energy of electrons ejected from matter by the photoelectric effect, i.e., as a direct result of absorption of energy from electromagnetic radiation. As the energies of the electrons are characteristic of a specific element, the measurement of the energy of these electrons is a technique used to determine the chemical composition of surfaces.

Penetrating electromagnetic radiation emitted when the inner orbital electrons of an atom are excited and release radiant energy. X-ray wavelengths range from 1 pm to 10 nm. Hard X-rays are the higher energy, shorter wavelength X-rays. Soft x-rays or Grenz rays are less energetic and longer in wavelength. The short wavelength end of the X-ray spectrum overlaps the GAMMA RAYS wavelength range. The distinction between gamma rays and X-rays is based on their radiation source.

Electric power supply devices which convert biological energy, such as chemical energy of metabolism or mechanical energy of periodic movements, into electrical energy.

Quick Search


DeepDyve research library

Searches Linking to this Article