Search results for "quantum theory"
showing 10 items of 234 documents
Simulating pump-probe photo-electron and absorption spectroscopy on the attosecond time-scale with time-dependent density-functional theory
2013
Molecular absorption and photoelectron spectra can be efficiently predicted with real-time time-dependent density functional theory. We show herein how these techniques can be easily extended to study time-resolved pump-probe experiments, in which a system response (absorption or electron emission) to a probe pulse is measured in an excited state. This simulation tool helps with the interpretation of fast-evolving attosecond time-resolved spectroscopic experiments, in which electronic motion must be followed at its natural timescale. We show how the extra degrees of freedom (pump-pulse duration, intensity, frequency, and time delay), which are absent in a conventional steady-state experimen…
The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.
2014
The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and…
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse…
2008
The great cost associated with the development of new anabolic-androgenic steroid (AASs) makes necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, quantum, and physicochemical molecular descriptors, plus linear discriminant analysis (LDA) were used to analyze the anabolic/androgenic activity of structurally diverse steroids and to discover novel AASs, as well as also to give a structural interpretation of their anabolic-androgenic ratio (AAR). The obtained models are able to correctly classify 91.67% (86.27%) of the AASs in the training (test) sets, respectively. The results of predictions on the 10% full-out cross-validation test al…
Iron’s Wake: The Performance of Quantum Mechanical-Derived Versus General-Purpose Force Fields Tested on a Luminescent Iron Complex
2020
Recently synthetized iron complexes have achieved long-lived excited states and stabilities which are comparable, or even superior, to their ruthenium analogues, thus representing an eco-friendly and cheaper alternative to those materials based on rare metals. Most of computational tools which could help unravel the origin of this large efficiency rely on ab-initio methods which are not able, however, to capture the nanosecond time scale underlying these photophysical processes and the influence of their realistic environment. Therefore, it exists an urgent need of developing new low-cost, but still accurate enough, computational methodologies capable to deal with the steady-state and trans…
On the impact of side methyl groups on the structure and vibrational properties of β-carotenoids. The case of butadiene and isoprene
2021
Abstract Theoretical consideration about the impact of methyl groups on the structure and vibrational properties of β-carotenoids, using medium size molecules of trans-butadiene and trans-isoprene, are reported. Density functional theory (DFT) calculations with correlation-consistent and polarization-consistent basis sets were applied to trans-1,3-butadiene and trans-isoprene as the smallest building bricks of β-carotenoids. Their structure and harmonic vibrations were estimated in the complete basis set limit (CBS) using the non-linear least square fit. Optimized geometries and harmonic frequencies, obtained with B3LYP and BLYP density functionals and large basis sets, were favorably repro…
Ibuprofen degradation using a Co-doped carbon matrix derived from peat as a peroxymonosulphate activator
2021
The wider presence of pharmaceuticals and personal care products in nature is a major cause for concern in society. Among pharmaceuticals, the anti-inflammatory drug ibuprofen has commonly been found in aquatic and soil environments. We produced a Co-doped carbon matrix (Co-P 850) through the carbonization of Co2+ saturated peat and used it as a peroxymonosulphate activator to aid ibuprofen degradation. The properties of Co-P 850 were analysed using field emission scanning electron microscopy, energy filtered transmission electron microscopy and X-ray photoelectron spectroscopy. The characterization results showed that Co/Fe oxides were generated and tightly embedded into the carbon matrix …
The catalytic mechanism of glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma cruzi elucidated via the QM/MM approach
2013
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) has been identified as a key enzyme involved in glycolysis processes for energy production in the Trypanosoma cruzi parasite. This enzyme catalyses the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) in the presence of inorganic phosphate (Pi) and nicotinamide adenosine dinucleotide (NAD+). The catalytic mechanism used by GAPDH has been intensively investigated. However, the individual roles of Pi and the C3 phosphate of G3P (Ps) sites, as well as some residues such as His194 in the catalytic mechanism, remain unclear. In this study, we have employed Molecular Dynamics (MD) simulations within hybrid quantum mechanical/molecular …
Theoretical studies of HIV-1 reverse transcriptase inhibition
2012
Computational methods for accurately calculating the binding affinity of a ligand for a protein play a pivotal role in rational drug design. We herein present a theoretical study of the binding of five different ligands to one of the proteins responsible for the human immunodeficiency virus type 1 (HIV-1) cycle replication; the HIV-1 reverse transcriptase (RT). Two types of approaches are used based on molecular dynamics (MD) simulations within hybrid QM/MM potentials: the alchemical free energy perturbation method, FEP, and the pathway method, in which the ligand is physically pulled away from the binding site, thus rendering a potential of mean force (PMF) for the binding process. Our com…
Molecular structures and vibrations of m-methylaniline in the S0 and S1 states studied by laser induced fluorescence spectroscopy and ab initio calcu…
2000
Abstract The UV fluorescence excitation and dispersed fluorescence spectra of a jet-cooled m-methylaniline have been obtained for the S1←S0 transition, in which some of the bands have been observed for the first time. The main spectral bands have been assigned by comparison with those of other relevant substituted benzenes. It was found that the spectra exhibit an important feature which is the internal rotation of the methyl group in the electronic ground and excited states. Ab initio calculations at MP2/6-31G* and CIS/6-31G* show that the optimized structure of m-methylaniline in the ground state is not planar with the amino group having sp3 hybridation-like character due to the existence…
2-Acylamino- and 2,4-bis(acylamino)pyrimidines as supramolecular synthons analysed by multiple non-covalent interactions. DFT, X-ray diffraction, and…
2012
Intermolecular interactions of ten 2-acylamino and 2,4-bis(acylamino)pyrimidines (7 of which are previously unknown) have been investigated by X-ray structural, quantum chemical (DFT), and NMR spectral methods. Especially the concentration dependencies of the (1)H NMR chemical shifts and titrations with other molecules capable of multiple hydrogen bonding provided useful information regarding their association via triple or quadruple hydrogen bonding, which is controlled by the conformational preferences of 2-acylamino- and 2,4-bis(acylamino)pyrimidines. On comparison of the properties of 2-acylamino- and 2,4-bis(acylamino)pyrimidines with the corresponding pyridines, an additional nitrogen…