Ab initio calculations of absorption spectra of large molecules in solution: coumarin C153.
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Computational Biology↗
Biomedical subjects
Vincenzo Barone
Publications and source records attributed to Vincenzo Barone.
Gas-phase chemistry of diphosphate anions as a tool to investigate the intrinsic requirements of phosphate ester enzymatic reactions: the [M1M2HP2O7]- ions.
Experimental studies on gaseous inorganic phosphate ions are practically nonexistent, yet they can prove helpful for a better understanding of the mechanisms of phosphate ester enzymatic processes. The present contribution extends our previous investigations on the gas-phase ion chemistry of diphosphate species to the [M(1)M(2)HP(2)O(7)](-) ions where M(1) and M(2) are the same or different and correspond to the Li, Na, K, Cs, and Rb cations. The diphosphate ions are formed by electrospray ionization of 10(-4) M solutions of Na(5)P(3)O(10) in CH(3)CN/H(2)O (1/1) and MOH bases or M salts as a source of M(+) cations. The joint application of mass spectrometric techniques and quantum-mechanical calculations makes it possible to characterize the gaseous [M(1)M(2)HP(2)O(7)](-) ions as a mixed ionic population formed by two isomeric species: linear diphosphate anion coordinated to two M(+) cations (group I) and [PO(3)M(1)M(2)HPO(4)](-) clusters (group II). The relative gas-phase stabilities and activation barriers for the isomerization I-->II, which depend on the nature of the M(+) cations, highlight the electronic susceptibility of P-O-P bond breaking in the active site of enzymes. The previously unexplored gas-phase reactivity of [M(1)M(2)HP(2)O(7)](-) ions towards alcohols of different acidity was investigated by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS). The reaction proceeds by addition of the alcohol molecule followed by elimination of a water molecule.
Anions↗
Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water.
The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.
Absorption↗
Development and validation of an integrated computational approach for the modeling of cw-ESR spectra of free radicals in solution: p-(methylthio)phenyl nitronylnitroxide in toluene as a case study.
In this work we address the interpretation, via an ab initio integrated computational approach, of continuous wave electron spin resonance (cw-ESR) spectra of p-(methylthio)phenyl nitronylnitroxide (MTPNN) dissolved in toluene. Our approach is based on the determination of the spin Hamiltonian, averaged with respect to fast vibrational motions, with magnetic tensor parameters (Zeeman and hyperfine tensors) characterized by quantum mechanical density functional calculations. The system is then described by a stochastic Liouville equation, with inclusion of diffusive rotational dynamics. Parametrization of diffusion rotational tensor is provided by a hydrodynamic model. Cw-ESR spectra of MTPNN are simulated for a wide range of temperatures (155-292 K) with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing structural and dynamic information on molecular systems.
Journal Article↗
Short-lived quinonoid species from 5,6-dihydroxyindole dimers en route to eumelanin polymers: integrated chemical, pulse radiolytic, and quantum mechanical investigation.
The transient species formed by oxidation of three dimers of 5,6-dihydroxyindole (1), a major building block of the natural biopolymer eumelanin, have been investigated. Pulse radiolytic oxidation of 5,5',6,6'-tetrahydroxy-2,4'-biindolyl (3) and 5,5',6,6'-tetrahydroxy-2,7'-biindolyl (4) led to semiquinones absorbing around 450 nm, which decayed with second-order kinetics (2k=2.8x10(9) and 1.4x10(9) M-1 s-1, respectively) to give the corresponding quinones (500-550 nm). 5,5',6, 6'-Tetrahydroxy-2,2'-biindolyl (2), on the other hand, furnished a semiquinone (lamdamax=480 nm) which disproportionated at a comparable rate (2k=3x10(9) M-1 s-1) to give a relatively stable quinone (lamdamax=570 nm). A quantum mechanical investigation of o-quinone, quinonimine, and quinone methide structures of 2-4 suggested that oxidized 2-4 exist mainly as 2-substituted extended quinone methide tautomers. Finally, an oxidation product of 3 was isolated for the first time and was formulated as the hydroxylated derivative 5 arising conceivably by the addition of water to the quinone methide intermediate predicted by theoretical analysis. Overall, these results suggest that the oxidation chemistry of biindolyls 2-4 differs significantly from that of the parent 1, whereby caution must be exercised before concepts that apply strictly to the mode of coupling of 1 are extended to higher oligomers.
Dimerization↗
Order parameters of alpha,omega-diphenylpolyenes in a nematic liquid crystal from an integrated computational and 13C NMR spectroscopic approach.
The orientational order parameters and conformational behavior of five relatively large rodlike molecules, biphenyl, trans-stilbene, 1,3-diphenyl-butadiene, 1,3,5-diphenyl-hexatriene, and 1,3,5,7-diphenyl-octatetraene, dissolved in the thermotropic liquid crystal ZLI-1167, have been studied using an integrated approach combining (13)C NMR measurements and quantum mechanical computations of carbon chemical shift tensors. Besides biphenyl, the phenyl moiety of all structures has been found to have a high rotational mobility in the temperature range of the present experiments. The rank-two order parameter in the nematic phase is found to increase steadily from the shortest to the longest term of the series at any temperature within the nematic range. The molecular biaxiality order parameter is found to be small and essentially constant with temperature, giving further support to the common assumption of effective uniaxiality for these probes.
Journal Article↗
A quantum mechanical/molecular dynamics/mean field study of acrolein in aqueous solution: analysis of H bonding and bulk effects on spectroscopic properties.
A novel molecular dynamics methodology recently proposed by our group [Rega et al., Chem. Phys. Lett. 422, 367 (2006)], which is based on an integrated hybrid potential rooted in high level quantum mechanical methods using localized basis functions and nonperiodic boundary conditions, has been applied to study acrolein in aqueous solution. The solute structural rearrangement and its hydrogen-bonding pattern due to the interactions with water have been analyzed in some detail. Moreover, the solvent effects on the UV n-->pi* vertical transition and on the NMR 13C and 17O shielding constants of acrolein have been investigated theoretically by performing a posteriori quantum mechanical calculations on a statistically significant number of snapshots extracted from both gas-phase and aqueous solution simulations. Results show that such effective computational strategy can be successfully used to improve our understanding, at atomic level, of important spectroscopic observables.
Journal Article↗
Radiation-induced formation of DNA intrastrand crosslinks between thymine and adenine bases: A theoretical approach.
The role of local geometric and stereo-electronic effects in tuning the radiation-induced formation of intrastrand crosslinks between adenine and thymine has been analyzed by a computational approach rooted in density functional theory. Our study points out that together with steric accessibility, stereo-electronic effects play a major role in determining the reaction mechanism and the observed predominance of the thymine-adenine lesion over the opposite sequence isomer.
Adenine↗
Evidence of variable H-bond network for nitroxide radicals in protic solvents.
This letter presents the results of a thorough computational investigation of two prototypical nitroxide spin probes in two different protic solvents, namely water and methanol, based on the combined use of Car-Parrinello molecular dynamic simulations and static cluster/continuum quantum chemical computations. Remarkable changes in solvation networks were found on going from aqueous to methanolic solutions. Moreover, despite their structural similarity, the two nitroxide probes display quite different behaviors in water. This provides a rationalization of indirect experimentally available indications. Eventually, the combination of static and dynamical ab initio methods exploited in the present study allows to dissect many subtle features of the nitroxide-solvent interaction, and also allows for an analysis of solvent effects on magnetic parameters (hyperfine coupling constants and g-tensor shift).
Letter↗
Toward an integrated computational approach to CW-ESR spectra of free radicals.
Interpretation of structural properties and dynamic behaviour of molecules in solution is of fundamental importance to understand their stability, chemical reactivity and catalytic action. Information can be gained, in principle, by a variety of spectroscopic techniques, magnetic as well as optical. In particular, continuous wave electron spin resonance (CW-ESR) measurements are highly informative. However, the wealth of structural and dynamic information which can be extracted from ESR spectroscopy is, at present, limited by the necessity of employing computationally efficient models, which are increasingly complex as they need to take into account diverse relaxation processes affecting the spectrum. In this paper, we address the basic theoretical tools needed to predict, essentially ab initio, CW-ESR spectra observables according to the stochastic Liouville equation (SLE) approach, combined with quantum mechanical and hybrid methods for the accurate and efficient computation of structural, spectroscopic and magnetic properties of molecular systems. We shall discuss, on one hand, the quantum mechanical calculation of magnetic observables, via density functional theory (DFT), time-dependent DFT (TD-DFT) and application of the polarizable continuum model (PCM) for the description of environmental effects, including anisotropic environments and systems where different regions are characterized by different dielectric constants. One the other hand, the explicit evaluation of dynamical effects will be discussed based on the numerically exact treatment of the SLE in the presence of several relaxation processes, which has been proven to be a challenging task.
Biomechanical Phenomena↗
A state-specific polarizable continuum model time dependent density functional theory method for excited state calculations in solution.
An effective state specific (SS) model for the inclusion of solvent effects in time dependent density functional theory (TD-DFT) computations of excited electronic states has been developed and coded in the framework of the so-called polarizable continuum model (PCM). Different relaxation time regimes can be treated thus giving access to a number of different spectroscopic properties together with solvent relaxation energies of paramount relevance in electron transfer processes. SS and conventional linear response (LR) models have been compared for two benchmark systems (coumarin 153 and formaldehyde in different solvents) and in the limiting simple case of a dipolar solute embedded in a spherical cavity. The results point out the complementarity of LR and SS approaches and the advantages of the latter model especially for polar solvents. The favorable scaling properties of PCM-TD-DFT models in both SS and LR variants and their availability in effective quantum mechanical codes pave the route for the computation of reliable spectroscopic properties of large molecules of technological and/or biological interest in their natural environments.
Biophysics↗
Vibrational analyses for CHFClBr and CDFClBr based on high level ab initio calculations.
Anharmonicity corrections to the harmonic vibrational spectra of CHFClBr and its deuterated isotopomer were computed by means of variational and perturbational approaches. A comparison of both methods is provided. Based on CCSD(T)/aug-cc-pVTZ electronic structure calculations excellent agreement with experimental data was obtained. Absolute mean deviations are in the range of about 4 cm(-1) for the fundamental modes, while slightly larger values of about 7 cm(-1) were found for the first vibrational overtones. In addition, vibrationally averaged structural parameters are provided for both molecules. The calculations will serve as a future starting point for parity-violation effects in vibrational transitions in these chiral molecules.
Journal Article↗
Solvent effect on the singlet excited-state dynamics of 5-fluorouracil in acetonitrile as compared with water.
The excited-state dynamics of 5-fluorouracil in acetonitrile has been investigated by femtosecond fluorescence upconversion spectroscopy in combination with quantum chemistry TD-DFT calculations ((PCM/TD-PBE0). Experimentally, it was found that when going from water to acetonitrile solution the fluorescence decay of 5FU becomes much faster. The calculations show that this is related to the opening of an additional decay channel in acetonitrile solution since the dark n/pi* excited state becomes near degenerate with the bright pi/pi* state, forming a conical intersection close to the Franck-Condon region. In both solvents, a S1-S0 conical intersection, governed by the out-of-plane motion of the fluorine atom, is active, allowing an ultrafast internal conversion to the ground state.
Acetonitriles↗
Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pK(a) calculations and molecular dynamics simulations.
A thorough study of the acid-base behavior of the four histidines and the other titratable residues of the structured domain of human prion protein (125-228) is presented. By using multi-tautomer electrostatic calculations, average titration curves have been built for all titratable residues, using the whole bundles of NMR structures determined at pH 4.5 and 7.0. According to our results, (1) only histidine residues are likely to be involved in the first steps of the pH-driven conformational transition of prion protein; (2) the pK(a)'s of His140 and His177 are approximately 7.0, whereas those of His155 and His187 are < 5.5. 10-ns long molecular dynamics simulations have been performed on five different models, corresponding to the most significant combinations of histidine protonation states. A critical comparison between the available NMR structures and our computational results (1) confirms that His155 and His187 are the residues whose protonation is involved in the conformational rearrangement of huPrP in mildly acidic condition, and (2) shows how their protonation leads to the destructuration of the C-terminal part of HB and to the loss of the last turn of HA that represent the crucial microscopic steps of the rearrangement.
Amino Acid Sequence↗
Dissociative electron transfer in donor-peptide-acceptor systems: results for kinetic parameters from a density functional/polarizable continuum model.
The main structural and electronic factors playing a role in intramolecular dissociative electron transfer of a simple donor-peptide-acceptor (D-peptide-A) model have been investigated by an integrated computational protocol based on the density functional theory, its time-dependent extension, and the polarizable continuum model. Our results allow us to elucidate the electronic states involved in the process and how they are perturbed by the orientation of the donor and the acceptor with respect to the peptide chain and by the presence of the solvent. We also report a semiquantitative estimation of the rate constant governing electron transfer obtained by a direct quantum mechanical evaluation of all the terms entering the kinetic expressions based on the Marcus theory and its extensions.
Electron Transport↗
A parameter-free quantum-mechanical approach for calculating electron-transfer rates for large systems in solution.
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Journal Article↗
Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells.
In this work, the mean field (MF) method, a continuum-based model designed for treating complex molecular systems, such as liquids and solutions, recently presented by Brancato et al. [J. Chem. Phys. 122, 154109 (2005)], has been further developed and improved especially in the treatment of the electrostatics. The revised model has been used to investigate the size effects on several physical properties of various solute-solvent systems by increasing the number of explicitly included solvent molecules from few tens up to thousands. Results on simple ions, such as sodium and chloride ions, and on a small peptide, such as alanine dipeptide analog (AcAlaNHMe), have shown that solvation structures and dynamics, as well as solvent-induced changes in the solute conformation, can be correctly reproduced by the MF model, providing that only two or three solvent layers are treated explicitly.
Journal Article↗
A polarizable continuum approach for the study of heterogeneous dielectric environments.
We present a computational method, exploiting some features of the polarizable continuum model (PCM) to describe heterogeneous media; it belongs to the family of electrostatic embedding mixed methods, such as the more common quantum-mechanical (QM)/molecular mechanics approaches, with the electrostatic long range effects accounted for by a polarized continuum instead of atomic point charges. Provided effective dielectric constants are determined for the various parts of the system, the method is much faster than its atomistic counterpart, and allows for high-level QM calculations on the fragment of interest, using all the highly efficient computational tools developed for homogeneous PCM. Two case studies (the calculation of the pKa of solvent exposed acidic residues in a model protein, and the calculation of the electron spin resonance spectrum of a typical spin probe partially embedded in a membrane) are analyzed in some detail, to illustrate the application of the method to complex systems.
Algorithms↗