Papers by Leonardo Guidoni
Biochimica et Biophysica Acta (BBA) - Biomembranes, 2002
We present a theoretical study on structural and electronic aspects of K + permeation through the... more We present a theoretical study on structural and electronic aspects of K + permeation through the binding sites of the KcsA channel's selectivity filter. Density functional calculations are carried out on models taken from selected snapshots of a molecular dynamics simulation recently reported [FEBS Lett. 477 (2000) 37]. During the translocation process from one binding site to the other, the coordination number of the permeating K + ion turns out to decrease and K + ion polarizes significantly its ligands, backbone carbonyl groups and a water molecule. K + -induced polarization increases significantly at the transition state (TS) between the two binding sites. These findings suggest that polarization effects play a significant role in the microscopic mechanisms regulating potassium permeation.
Journal of Chemical Theory and Computation, Aug 6, 2008
We present a Quantum Monte Carlo study of the dissociation energy and the dispersion curve of the... more We present a Quantum Monte Carlo study of the dissociation energy and the dispersion curve of the water dimer, a prototype of hydrogen bonded system. Our calculations are based on a wave function which is a modern and fully correlated implementation of the Pauling's valence bond idea: the Jastrow Antisymmetrised Geminal Power (JAGP) [Casula et al J.Chem.Phys. 119,6500-6511 (2003)]. With this variational wave function we obtain a binding energy of -4.5(0.1) kcal/mol, that is only slightly increased to -4.9(0.1) kcal/mol by using the Lattice Regularized Diffusion Monte Carlo (LRDMC). This projection technique allows to improve substantially the correlation energy of a given variational guess and indeed, when applied to the JAGP, yields a binding energy in fair agreement with the value of -5.0 kcal/mol reported by experiments and other theoretical works. The minimum position, the curvature and the asymptotic behavior of the dispersion curve are well reproduced both at the variational and LRDMC level. Moreover, thanks to the simplicity and the accuracy of our variational approach, we are able to dissect the various contributions to the binding energy of the water dimer in a systematic and controlled way. This is achieved by appropriately switching off determinantal and Jastrow variational terms in the JAGP. Within this scheme, we estimate that the van der Waals contribution to the electron correlation is substantial and amounts to 1.5(0.2) kcal/mol, this value being comparable with the intermolecular covalent energy, that we find to be 1.1(0.2) kcal/mol. The present Quantum Monte Carlo approach based on the JAGP wavefunction reveals as a promising tool for the interpretation and the quantitative description of weakly interacting systems, where both dispersive and covalent energy contributions play an important role.
Photosynthesis fuels life on Earth by storing solar energy in chemical form, inspiring technologi... more Photosynthesis fuels life on Earth by storing solar energy in chemical form, inspiring technological schemes for sustainable fuel production. Today’s oxygen-rich atmosphere results from photosynthetic O2-production during water-splitting at the protein-bound manganese cluster of photosystem II. Formation of the O2 molecule starts from a state with four accumulated electron holes, the S4-state, postulated half a century ago1 and remaining enigmatic ever since. Here we resolve this missing key element in photosynthetic O2-formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combing these results with computational chemistry reveals that in S4 not only are four electron holes accumulated by metal ion and protein sidechain oxidation, but also a crucial proton vacancy is created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in an astonishing single-e...
Physical Chemistry Chemical Physics, 2018
IRMPD spectra and calculations reveal the binding motifs of halide ions to tyrosine and its nitro... more IRMPD spectra and calculations reveal the binding motifs of halide ions to tyrosine and its nitro derivative, 3-nitro-tyrosine.
Physical Review B, 1998
Fixed-node Green's function Monte Carlo calculations have been performed for very large 16×16 2D ... more Fixed-node Green's function Monte Carlo calculations have been performed for very large 16×16 2D Hubbard lattices, large interaction strengths U = 10, 20, and 40, and many (15 ∼ 20) densities between empty and half filling. The nodes were fixed by a simple Slater-Gutzwiller trial wavefunction. For each value of U we obtained a sequence of ground-state energies which is consistent with the possibility of a phase separation close to half-filling, with a hole density in the hole-rich phase which is a decreasing function of U . The energies suffer, however, from a fixed-node bias: more accurate nodes are needed to confirm this picture. Our extensive numerical results and their test against size, shell, shape and boundary condition effects also suggest that phase separation is quite a delicate issue, on which simulations based on smaller lattices than considered here are unlikely to give reliable predictions.
Journal of Chemical Theory and Computation, 2011
We present an extensive investigation of the vertical excitations of the anionic and neutral form... more We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophoreÀprotein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore.
The Journal of Chemical Physics, 2012
The description of the electronic structure and magnetic properties of multi-centers transition m... more The description of the electronic structure and magnetic properties of multi-centers transition metal complexes, especially of mixed-valence compounds, still represents a challenge for density functional theory (DFT) methods. The energies and the geometries of the correctly symmetrized low-spin ground state are estimated using the Heisenberg-Dirac-van Vleck spin Hamiltonian within the extended broken symmetry method introduced by Marx and co-workers [Nair et al., J. Chem. Theory Comput. 4, 1174–1188 (2008)10.1021/ct800089x]. In the present work we extend the application of this technique, originally implemented using the DFT+U scheme, to the use of hybrid functionals, investigating the ground-state properties of di-iron and di-manganese compounds. The calculated magnetic coupling and vibrational properties of ferredoxin molecular models are in good agreements with experimental results and DFT+U calculations. Six different mixed-valence Mn(III)–Mn(IV) compounds have been extensively ...
International Journal of Mass Spectrometry, 2013
The ESI-formed protonated 2 -deoxycytidine, cytidine, cytarabine, and gemcitabine have been probe... more The ESI-formed protonated 2 -deoxycytidine, cytidine, cytarabine, and gemcitabine have been probed using infrared multiphoton dissociation (IRMPD) spectroscopy performed in the 900-2000 cm -1 region at CLIO, the Orsay Free Electron Laser facility, and in the 2800-3800 cm -1 region using a YAG-laser coupled to a table-top optical parametric oscillator/amplifier (OPO/OPA). The IRMPD spectra are compared of the protonated nucleosides with the IR spectra of their B3LYP/6-311++G(d,p)-optimized isomeric forms. The stability at room temperature of some conformers has been investigated by means of ab initio molecular dynamics simulations. The IRMPD spectra are consistent with the formation in the ESI source of both the N3and the O2-protonated nucleosides. The most favoured members of both families are characterized by the pyrimidine base oriented anti to the furanose moiety. Concerning the O2-protonated nucleosides, IRMPD spectra and thermochemical considerations support the predominant formation of the structures with the proton oriented up relative to the furanose moiety.
Journal of Chemical Theory and Computation, Aug 6, 2008
We present a Quantum Monte Carlo study of the dissociation energy and the dispersion curve of the... more We present a Quantum Monte Carlo study of the dissociation energy and the dispersion curve of the water dimer, a prototype of hydrogen bonded system. Our calculations are based on a wave function which is a modern and fully correlated implementation of the Pauling's valence bond idea: the Jastrow Antisymmetrised Geminal Power (JAGP) [Casula et al J.Chem.Phys. 119,6500-6511 (2003)]. With this variational wave function we obtain a binding energy of -4.5(0.1) kcal/mol, that is only slightly increased to -4.9(0.1) kcal/mol by using the Lattice Regularized Diffusion Monte Carlo (LRDMC). This projection technique allows to improve substantially the correlation energy of a given variational guess and indeed, when applied to the JAGP, yields a binding energy in fair agreement with the value of -5.0 kcal/mol reported by experiments and other theoretical works. The minimum position, the curvature and the asymptotic behavior of the dispersion curve are well reproduced both at the variational and LRDMC level. Moreover, thanks to the simplicity and the accuracy of our variational approach, we are able to dissect the various contributions to the binding energy of the water dimer in a systematic and controlled way. This is achieved by appropriately switching off determinantal and Jastrow variational terms in the JAGP. Within this scheme, we estimate that the van der Waals contribution to the electron correlation is substantial and amounts to 1.5(0.2) kcal/mol, this value being comparable with the intermolecular covalent energy, that we find to be 1.1(0.2) kcal/mol. The present Quantum Monte Carlo approach based on the JAGP wavefunction reveals as a promising tool for the interpretation and the quantitative description of weakly interacting systems, where both dispersive and covalent energy contributions play an important role.
Journal of Chemical Physics, Apr 14, 2015
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the ear... more Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.
Bulletin of the American Physical Society, Mar 12, 2008
We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) st... more We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) study of the binding energy and dispersion curve of the water dimer. One the aim of the present work is to investigate how the bonding of two water molecules, as a prototype of the hydrogen-bonded complexes, could be described by a JAGP wave function, an implementation of the resonating valence bond idea.Using a pseudopotential for the inert core of the Oxygen, with a full optimization of the variational parameters, we obtain at the VMC level a binding energy of -4.5(0.1) Kcal/mol, while LRDMC gives -4.9(0.1)Kcal/mol (exp. 5 Kcal/Mol). The calculated dispersion curve reproduces both at the VMC and LRDMC level the miminum position and the right curvature.The quality of the WF gives us the possibility to dissect the binding energy in different contributions by appropriately switching off determinantal and Jastrow terms in the JAGP: we estimate the dynamical contribution to the binding energy of the order of 1.4(0.2) Kcal/Mol whereas the covalent one about 1.0(0.2) Kcal/Mol. JAGP reveales thus a promising WF for describing systems where dispersive and covalent forces play an important role
Journal of Chemical Theory and Computation, Aug 23, 2017
The structures of three negatively charged forms (anionic keto-1 and enol-1, dianonic enol-2) of ... more The structures of three negatively charged forms (anionic keto-1 and enol-1, dianonic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S 1 ← S 0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2 and many body Green's function Theory (MBGFT). The use of MBGFT, by means of the Bethe-Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with
Journal of Chemical Theory and Computation, 2017
The structures of three negatively charged forms (anionic keto-1 and enol-1, dianonic enol-2) of ... more The structures of three negatively charged forms (anionic keto-1 and enol-1, dianonic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S 1 ← S 0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2 and many body Green's function Theory (MBGFT). The use of MBGFT, by means of the Bethe-Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with
The Journal of Chemical Physics, 2016
The correct description of the ground state electronic and geometrical properties of multi-centre... more The correct description of the ground state electronic and geometrical properties of multi-centre transition metal complexes necessitates of a high-level description of both dynamical and static correlation effects. In di-metallic complexes, the ground state low spin properties can be computed starting from single-determinants High-Spin (HS) and Broken Symmetry (BS) states by reconstructing an approximated low spin potential energy surface through the extended broken symmetry approach, based on the Heisenberg Hamiltonian. In the present work, we first apply this approach within the variational Monte Carlo method to tackle the geometry optimization of a Fe2S2(SH)42− model complex. To describe the HS and BS wavefunctions, we use a fully optimized unrestricted single determinant with a correlated Jastrow factor able to recover a large amount of dynamical correlation. We compared our results with those obtained by density functional theory and other multiconfigurational approaches, disc...
Journal of Chemical Theory and Computation, 2016
Journal of Chemical Theory and Computation, 2015
Due to the crucial role played by electron correlation, the accurate determination of ground stat... more Due to the crucial role played by electron correlation, the accurate determination of ground state geometries of π-conjugated molecules is still a challenge for many quantum chemistry methods. Because of the high parallelism of the algorithms and their explicit treatment of electron correlation effects, Quantum Monte Carlo calculations can offer an accurate and reliable description of the electronic states and of the geometries of such systems, competing with traditional quantum chemistry approaches. Here, we report the structural properties of polyacetylene chains H-(C 2 H 2 ) N -H up to N = 12 acetylene units, by means of Variational Monte Carlo (VMC) calculations based on the multi-determinant Jastrow Antisymmetrized Geminal Power (JAGP) wave function. This compact ansatz can provide for such systems an accurate description of the dynamical electronic correlation as recently detailed for the 1,3-butadiene molecule [J. Chem. Theory Comput. 2015 11 (2), 508-517]. The calculated Bond Length Alternation (BLA), namely the difference between the single and double carbon bonds, extrapolates, for N → ∞, to a value of 0.0910(7) Å, compatible with the experimental data. An accurate analysis was able to distinguish between the influence of the multi-determinantal AGP expansion and of the Jastrow factor on the geometrical properties of the fragments. Our size-extensive and self-interaction-free results provide new and accurate ab initio references for the structures of the ground state of polyenes.
Journal of Chemical Theory and Computation, 2015
We investigate the effects of the static and dynamical electronic correlations on the level of co... more We investigate the effects of the static and dynamical electronic correlations on the level of conjugation of the trans-1,3butadiene molecule through Quantum Monte Carlo methods applied to an Antisymmetrized Geminal Power (AGP) wave function, with a Jastrow factor similar to the Gutzwiller ansatz. The degree of conjugation is measured through the convergence of the structural properties of 1,3-butadiene and in particular of the Bond Length Alternation (BLA), that is the difference between the lengths of the single and double carbon bonds. After verifying the different roles of the Fermionic AGP part of our wave function and of the Jastrow factor in recovering electronic correlation, we study the effects of a constrained Active Space AGP (AGP AS ), similar to that used in the Complete Active Space (CAS) representation. Through this AGP AS , we are able to identify the effect of the limited active space on the degree of conjugation, showing that in the limit of infinite active space the structural properties converge exactly to those of the atomic AGP, giving a BLA for 1,3-butadiene around 0.1244(5) Å.
Journal of chemical theory and computation, Jan 10, 2015
The penta-2,4-dieniminium cation (PSB3) displays similar ground state and first excited state pot... more The penta-2,4-dieniminium cation (PSB3) displays similar ground state and first excited state potential energy features as those of the retinal protonated Schiff base (RPSB) chromophore in rhodopsin. Recently, PSB3 has been used to benchmark several electronic structure methods, including highly correlated multireference wave function approaches, highlighting the necessity to accurately describe the electronic correlation in order to obtain reliable properties even along the ground state (thermal) isomerization paths. In this work, we apply two quantum Monte Carlo approaches, the variational Monte Carlo and the lattice regularized diffusion Monte Carlo, to study the energetics and electronic properties of PSB3 along representative minimum energy paths and scans related to its thermal cis-trans isomerization. Quantum Monte Carlo is used in combination with the Jastrow antisymmetrized geminal power ansatz, which guarantees an accurate and balanced description of the static electronic ...
The Journal of chemical physics, Jan 7, 2014
The electronic properties of the oxygen molecule, in its singlet and triplet states, and of many ... more The electronic properties of the oxygen molecule, in its singlet and triplet states, and of many small oxygen-containing radicals and anions have important roles in different fields of chemistry, biology, and atmospheric science. Nevertheless, the electronic structure of such species is a challenge for ab initio computational approaches because of the difficulties to correctly describe the statical and dynamical correlation effects in presence of one or more unpaired electrons. Only the highest-level quantum chemical approaches can yield reliable characterizations of their molecular properties, such as binding energies, equilibrium structures, molecular vibrations, charge distribution, and polarizabilities. In this work we use the variational Monte Carlo (VMC) and the lattice regularized Monte Carlo (LRDMC) methods to investigate the equilibrium geometries and molecular properties of oxygen and oxygen reactive species. Quantum Monte Carlo methods are used in combination with the Jas...
We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) st... more We present a variational MonteCarlo (VMC) and lattice regularized diffusion MonteCarlo (LRDMC) study of the binding energy and dispersion curve of the water dimer. One the aim of the present work is to investigate how the bonding of two water molecules, as a prototype of the hydrogen-bonded complexes, could be described by a JAGP wave function, an implementation of the resonating valence bond idea.Using a pseudopotential for the inert core of the Oxygen, with a full optimization of the variational parameters, we obtain at the VMC level a binding energy of -4.5(0.1) Kcal/mol, while LRDMC gives -4.9(0.1)Kcal/mol (exp. 5 Kcal/Mol). The calculated dispersion curve reproduces both at the VMC and LRDMC level the miminum position and the right curvature.The quality of the WF gives us the possibility to dissect the binding energy in different contributions by appropriately switching off determinantal and Jastrow terms in the JAGP: we estimate the dynamical contribution to the binding energy...
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Papers by Leonardo Guidoni