Search results for "Computation"
showing 10 items of 7362 documents
Short hydrogen bonds enhance nonaromatic protein-related fluorescence
2021
Significance Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.
Insights on the origin of catalysis on glycine N-methyltransferase from computational modeling.
2018
The origin of enzyme catalysis remains a question of debate despite much intense study. We report a QM/MM theoretical study of the SN2 methyl transfer reaction catalyzed by a glycine N-methyltransferase (GNMT) and three mutants to test whether recent experimental observations of rate-constant reductions and variations in inverse secondary α-3H kinetic isotope effects (KIEs) should be attributed to changes in the methyl donor−acceptor distance (DAD): is catalysis due to a compression effect? Semiempirical (AM1) and DFT (M06-2X) methods were used to describe the QM subset of atoms, while OPLS-AA and TIP3P classical force fields were used for the protein and water molecules, respectively. The …
Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2
2016
The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess t…
Adhesion trends and growth mode of ultra-thin copper films on MgO
2004
Ab initio simulations are performed for Cu atoms adsorbed on the perfect MgO(001) substrate, with an ordered metal coverage varied from 1 monolayer (ML), i.e. almost single atoms, up t o1M L. As trong dependence of the adhesion energy and the sub-monolayer film distance from the substrate on the surface coverage and adsorbate positions (Mg 2+ or O 2− )i s discussed. The nature of interfacial bonding at all coverages is physisorption .W hen increasing Cu atomic fraction, a decrease of the substrate-induced polarization of adatoms accompanied by an increase of both in-plane metallic bonding and the interfacial distance has been found. Combining results of ab initio calculations with thermodyn…
An ab initio CI study on the rotational barrier of the allyl anion
1986
All-electron and pseudopotential non-empirical calculations have been performed on C 2v and C s (syn, anti) allyl anion conformations. Using a double-zeta valence-shell basis set within the Epstein-Nesbet definition of the unperturbed Hamiltonian, a value about 19 kcal/mol is found for the barrier to rotation of the allyl anion. This value is the theoretical value obtained with greater accuracy, and the lowest one for the rotational barrier.
Metal film growth on regular and defective MgO(001) surface: A comparative ab initio simulation and thermodynamic study
2006
Abstract In order to understand the difference in metallic film growth modes on perfect and defective oxide substrates, we have combined ab initio B3LYP periodic calculations on the slab models of the corresponding Me/MgO(0 0 1) interfaces (Me = Ag, Cu) with thermodynamic theory of solid solutions. For a defectless magnesia surface, we confirm the experimentally observed submonolayer growth of 3D metallic islands (Ag possesses a higher trend than Cu). Formation of Fs centers (neutral O vacancies) on the substrate markedly enhances metal atom adsorption as compared to physisorption over regular sites on a defect-free substrate. For the first time, we predict that the presence of these surfac…
Dielectric friction effects on rotational reorientation of three cyanine dyes in n-alcohol solutions
1997
We have estimated the effect of dielectric friction on the rotational correlation times of three cationic cyanine dyes. Dielectric corrections were evaluated by using the Stokes–Einstein-Debye hydrodynamic continuum model including the dielectric friction for DiIC2, DiIC6, and DiIC14 in different n-alcohol solutions at room temperature. The dielectric corrections were done to cis and trans conformations of the cyanine dyes. For the trans conformations, which were found more stable than cis conformations, the dielectric model seemed to be more properly suited. The ground and excited state dipole moments for the calculations were evaluated from ab initio molecular orbital calculations and for…
Geometric Structure and Torsional Potential of Biisothianaphthene. A Comparative DFT and ab Initio Study
1997
We present a study of the torsional potential of biisothianaphthene and compare it to that of bithiophene. The calculations are performed at the ab initio and semiempirical Hartree−Fock (HF), ab initio post-Hartree−Fock, and density functional theory (DFT) levels. Our study has two major aims: (i) on the physico-chemical side, to asses the optimal conformation of biisothianaphthene and evaluate the rotational barriers toward coplanar structures and (ii) on the methodological side, to asses the usefulness of DFT approaches. In contrast to previous estimates, the torsional potential of biisothianaphthene is found to differ markedly from that of bithiophene. For biisothianaphthene, strongly r…
Experimental Investigations and Ab Initio Studies of Tellurium(II) Dithiolates, Te(SR)2
1999
The reaction between Te(O(i)Pr)(4) and HSR offers a new and effective route to tellurium dithiolates, Te(SR)(2). Te(S(i)Pr)(2) (1) and Te(S(t)Bu)(2) (2) are stable compounds whereas Te(SPh)(2) (3) slowly decomposes at room temperature to give Te and Ph(2)S(2). IR spectra of 1-3 and ab initio calculations (HF/3-21G(d) and MP2 with double-zeta polarization effective core potential basis set) show nu(as)(Te-S) and nu(s)(Te-S) to be around 340 and 380 cm(-)(1), respectively. UV spectra exhibit similar lambda(max) (346-348 nm) for all three compounds, with the greater extinction coefficient of 3 accounting for its different and more intense color. Analysis of the molecular orbitals of the model …
Vibrations of a single adsorbed organic molecule: anharmonicity matters!
2010
Vibrational spectroscopy is a powerful tool to identify molecules and to characterise their chemical state. Inelastic electron tunnelling spectroscopy (IETS) combined with scanning tunnelling microscopy (STM) allows the application of vibrational analysis to a single molecule. Up to now, IETS was restricted to small species due to the complexity of vibration spectra for larger molecules. We extend the horizon of IETS for both experiment and theory by measuring the STM-IETS spectra of mercaptopyridine adsorbed on the (111) surface of gold and comparing it to theoretical spectra. Such complex spectra with more than 20 lines can be reliably determined and computed leading to completely new ins…