Search results for "kvanttikemia"

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

2019

The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that …

Computational approach to design of aptamers to the receptor binding domain of SARS-CoV-2

2021

The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, th…

Theory for the stationary polariton response in the presence of vibrations

2019

We construct a model describing the response of a hybrid system where the electromagnetic field - in particular, surface plasmon polaritons - couples strongly with electronic excitations of atoms or molecules. Our approach is based on the input-output theory of quantum optics, and in particular it takes into account the thermal and quantum vibrations of the molecules. The latter is described within the $P(E)$ theory analogous to that used in the theory of dynamical Coulomb blockade. As a result, we are able to include the effect of the molecular Stokes shift on the strongly coupled response of the system. Our model then accounts for the asymmetric emission from upper and lower polariton mod…

Multi-scale dynamics simulations of molecular polaritons: The effect of multiple cavity modes on polariton relaxation

2021

It is included two versions of this item: the Accepted Version which is already Open Access and the Published Version which is under an embargo period till 2022-03-09.

Multiscale Molecular Dynamics Simulations of Polaritonic Chemistry.

2017

When photoactive molecules interact strongly with confined light modes as found in plasmonic structures or optical cavities, new hybrid light-matter states can form, the so-called polaritons. These polaritons are coherent superpositions (in the quantum mechanical sense) of excitations of the molecules and of the cavity photon or surface plasmon. Recent experimental and theoretical works suggest that access to these polaritons in cavities could provide a totally new and attractive paradigm for controlling chemical reactions that falls in between traditional chemical catalysis and coherent laser control. However, designing cavity parameters to control chemistry requires a theoretical model wi…

Saturation vapor pressure characterization of selected low-volatility organic compounds using a residence time chamber

2023

Saturation vapor pressure (psat) is an important thermodynamic property regulating the gas-to-particle partitioning of organic compounds in the atmosphere. Low-volatility organic compounds (LVOCs), with sufficiently low psat values, primarily stay in the particle phase and contribute to aerosol formation. Obtaining accurate information on the psat of LVOCs requires volatility measurements performed at temperatures relevant to atmospheric aerosol formation. Here, we present an isothermal evaporation method using a residence time chamber to measure psat for dry single-compound nanoparticles at 295 K. Our method is able to characterize organic compounds with psat spanning from 10−8 to 10−4 Pa …

Self-assembly of new cobalt complexes based on [Co(SCN)4], synthesis, empirical, antioxidant activity, and quantum theory investigations

2022

The cobalt (II) complexes have been synthesized from the reaction of the cationic entities (3,4-dimethylaniline (1) and histamine (2)) with metallic salt CoCl2⋅6H2O and thiocyanate ion (SCN−) as a ligand in H2O/ethanolic solution and processing by the evaporation crystal growth method at room temperature to get crystals. The synthesized complex has been fully characterized by single-crystal X-ray diffraction. UV–Visible, FTIR spectroscopy, TGA analysis, and DFT circulations were also performed. The crystal structural analysis reveals that the solid (1) {[Co(SCN)4] (C8H12N)3}·Cl crystallizes in the monoclinic system with the space group P21/n and the solid (2) {[Co(SCN)4](C5H11N3)2}·2Cl crys…

Theoretical characterization of the photochemical reaction CO2+O(3P)→CO+O2 related to experiments in solid krypton

2020

Formation and decomposition of the complex of carbon dioxide and atomic oxygen are characterized by quantum chemistry methods aiming to rationalize experimental studies in solid krypton. The observed FTIR spectra reflected the temporal evolution of the system after irradiation showing the bands of reactants, intermediates and products. Advanced quantum chemistry calculations show that the T-shape complex CO2…O(3P) can be formed in the matrix. Its excitation by the 193 nm light results in the charge-transfer state CO2+…O-, which evolves to the reaction intermediate CO3. The latter species decomposes to CO + O2 following pathways on the excited state energy surfaces. peerReviewed

Elektroniset aaltopaketit atomeissa ja pienissä molekyyleissä

2005

Developments in many-body theory of quantum transport and spectroscopy with non-equilibrium Green's functions and time-dependent density functional t…

2015

The problem of quantum dynamics in open systems has gained attention in recent decades and not the least due to the advances made in quantum transport in molecular systems. The main motivation behind quantum transport and molecular electronics is the futuristic goal to be able at some point to replace, or to complement, the silicon-based technology and to make the electronic devices faster. On a fundamental level, one has to deal with time-dependent processes where electron-electron or electron- phonon interactions are of great importance, and they can cause profound quantitative and qualitative changes on the physical and dynamical properties of electronic systems compared to the non-inter…