Leonardo Guidoni

• PhD
• Professor (Associate) at University of L'Aquila

Quantum algorithms based on the variational principle have found applications in diverse areas with a huge flexibility. But as the circuit size increases the variational landscapes become flattened, causing the so-called Barren plateau phenomena. This will lead to an increased difficulty in the optimization phase, due to the reduction of the cost f...

The aim of this paper is enlarging the potential use of ZIF‐8 MOF as drug delivery system (DDS) for antimicrobial molecules, in particular for sulfathiazole, to be employed for the treatment of Sub‐Acute Ruminal Acidosis (SARA) in dairy cows. We therefore optimized (from milligrams to grams) the synthesis methodology for ZIF‐8 MOF, moving from orga...

Light-driven water splitting by plants, algae and cyanobacteria is pivotal for global bioenergetics and biomass formation. A manganese cluster bound to the photosystem-II proteins catalyzes the complex reaction at high rate, but the rate-determining factors are insufficiently understood. Here we traced the oxygen-evolution transition by time-resolv...

In recent years Quantum Computing prominently entered in the field of Computational Chemistry, importing and transforming computational methods and ideas originally developed within other disciplines, such as Physics, Mathematics and Computer Science into algorithms able to estimate quantum properties of atoms and molecules on present and future qu...

Quantum algorithms based on the variational principle have found applications in diverse areas with a huge flexibility. But as the circuit size increases the variational landscapes become flattened, causing the so-called Barren plateau phenomena. This will lead to an increased difficulty in the optimization phase, due to the reduction of the cost f...

Vibrational spectroscopy serves as a powerful tool for characterizing intermediate states within the Kok–Joliot cycle. In this study, we employ a QM/MM molecular dynamics framework to calculate the room temperature infrared absorption spectra of the S1, S2, and S3 states via the Fourier transform of the dipole time auto-correlation function. To bet...

Exploiting the invariance of the molecular Hamiltonian by unitary transformation of the orbitals it is possible to significantly shorter the depth of the variational circuit in Variational Quantum Eigensolver (VQE) approach by using the Wavefunction-Adapted Hamiltonian Through Orbital Rotation (WAHTOR) algorithm. In this work, we introduce a non-ad...

State-of-the-art noisy digital quantum computers can only execute short-depth quantum circuits. Variational algorithms are a promising route to unlock the potential of noisy quantum computers since the depth of the corresponding circuits can be kept well below hardware-imposed limits. Typically, the variational parameters correspond to virtual RZ g...

Natural orbitals, defined in electronic structure and quantum chemistry as the (molecular) orbitals diagonalizing the one-particle reduced density matrix of the ground state, have been conjectured for decades to be the perfect reference orbitals to describe electron correlation. In the present work we applied the Wavefunction-Adapted Hamiltonian Th...

Deep eutectic solvents (DESs) are mixtures of two or more pure compounds (e.g., Lewis or Brønsted acids and bases, anionic and/or cationic species) in a well-defined stoichiometric proportion, with a melting point lower to that of an ideal liquid mixture. These neoteric solvents are highly tunable through varying the structure or relative ratio of...

By exploiting the invariance of the molecular Hamiltonian by a unitary transformation of the orbitals it is possible to significantly shorter the depth of the variational circuit in the Variational Quantum Eigensolver (VQE) algorithm by using the Wavefunction Adapted Hamiltonian Through Orbital Rotation (WAHTOR) algorithm. This work introduces a no...

Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today’s oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state—which was postulated...

The σ1 receptor (σ1-R) is an enigmatic endoplasmic reticulum resident transmembrane protein implicated in a variety of central nervous system disorders and whose agonists have neuroprotective activity. In spite of σ1-R’s physio-pathological and pharmacological importance, two of the most important features required to fully understand σ1-R function...

State-of-the-art noisy digital quantum computers can only execute short-depth quantum circuits. Variational algorithms are a promising route to unlock the potential of noisy quantum computers since the depth of the corresponding circuits can be kept well below hardware-imposed limits. Typically, the variational parameters correspond to virtual $R_Z...

Oligogalacturonides (OGs) are pectin fragments released from the breakdown of the homogalacturonan during pathogenesis that act as Damage-Associated Molecular Patterns. OG-oxidase 1 (OGOX1) is an Arabidopsis berberine bridge enzyme-like (BBE-l) oligosaccharide oxidase that oxidizes OGs, impairing their elicitor activity and concomitantly releasing...

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...

The structure of a decanuclear photo‐ and redox‐active dendrimer based on Ru(II) polypyridine subunits, suitable as a light‐harvesting multicomponent species for artificial photosynthesis, has been investigated by means of computer modelling. The compound has the general formula [Ru{(μ‐dpp)Ru[(μ‐dpp)Ru(bpy)2]2}3](PF6)20 (Ru10; bpy=2,2′‐bipyridine;...

In the first steps of natural oxygenic photosynthesis, sunlight is used to oxidize water molecules to protons, electrons and molecular oxygen. This reaction takes place on the Mn4Ca cluster located in the reaction centre of Photosystem II (PSII), where the cluster is assembled and continuously repaired through a process known as photoactivation. Un...

During the infection, plant cells secrete different OG-oxidase (OGOX) paralogs, defense flavoproteins that oxidize the oligogalacturonides (OGs), homogalacturonan fragments released from the plant cell wall that act as Damage Associated Molecular Patterns. OGOX-mediated oxidation inactivates their elicitor nature, but on the other hand makes OGs le...

Background Huntington’s Disease (HD) is a devastating and presently untreatable neurodegenerative disease, characterized by progressively disabling motor and mental manifestations. Sigma-1 receptor (σ1R), whose 3D structure has been recently determined by X-ray crystallography, is expressed in the central nervous system, and σ1R agonists have been...

We propose a modification of the Variational Quantum Eigensolver algorithm for electronic structure optimization using quantum computers, named non-unitary Variational Quantum Eigensolver (nu-VQE), in which a non-unitary operator is combined with the original system Hamiltonian leading to a new variational problem with a simplified wavefunction Ans...

Background Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C...

Water-oxidizing metal-(hydr)oxo catalyst films can be generally deposited and activated by applying a positive electrochemical potential to suitable starting aqueous solutions. Here, we used ab initio simulations based on density functional theory to investigate the initial formation process of hydroxo and oxo bridges between divalent transition me...

Metal–ligand cluster ions are structurally characterized by means of gas-phase infrared multiple photon dissociation spectroscopy. The mass-selected complexes consist of one or two metal cations M³⁺ (M = Al, Fe, or Ru) and two to five anionic bidentate acetylacetonate ligands. Experimental IR spectra are compared with different density functional t...

Calculations of relaxed geometries of multi-centre transition metal compounds are routinely carried out using Broken Symmetry Density Functional Theory. The resulting low-spin open shell electronic state is described by one single determinant and is affected by spin contamination. To alleviate this symmetry breaking, Extended Broken Symmetry (EBS)...

GabR is a bacterial transcription regulator with a dimeric structure in which each subunit includes a wHTH (winged Helix-Turn-Helix) domain connected through a peptide linker to a large C-terminal domain folded as the enzyme aspartate aminotransferase (AAT). In Bacillus subtilis, GabR activates the genes involved in the metabolism of γ-amino butyri...

Water oxidation occurring in oxygenic natural photosynthesis is catalyzed by the protein-cofactor complex Photosystem II. The catalytic cycle leading to the water splitting into protons, electrons and molecular oxygen, consists of five consecutive steps, namely S0-S4. Here, using QM/MM Molecular Dynamics simulations, we characterized structural and...

GabR from Bacillus subtilis is a transcriptional regulator of the MocR subfamily of GntR regulators. The MocR architecture is characterized by the presence of an N-terminal winged-Helix-Turn-Helix domain and a C-terminal domain folded as the pyridoxal 5′-phosphate (PLP) dependent aspartate aminotransferase (AAT). The two domains are linked by a pep...

Photosynthetic water oxidation is catalyzed by the Mn4Ca cluster in Photosystem II (PSII). The nearby redox-active tyrosine (YZ) serves as a direct electron acceptor of the Mn4Ca cluster and it forms a low-barrier H-bond (LBHB) with a neighboring histidine residue (D1-His190). Experimental evidences indicate that YZ oxidation is triggering changes...

Bio‐inspired catalysis for artificial photosynthesis has been widely studied for decades, in particular, with the purpose of using bio‐disposable and non‐toxic metals as building blocks. The characterisation of such catalysts has been achieved by using different kinds of spectroscopic methods, from X‐ray crystallography to NMR spectroscopy. An arti...

Understanding the structural modification experienced by the Mn 4CaO 5 oxygen evolving complex of Photosystem II along the Kok‐Joliot’s cycle is a challenge for both theory and experiments since many decades. In particular, differential infrared spectroscopy was extensively used to probe the surroundings of the reaction centre, to catch spectral ch...

Understanding the mechanism for electrochemical water-oxidation is important for the development of more efficient catalysts for artificial photosynthesis. A basic step is the proton-coupled electron transfer, which enables accumulation of oxidizing equivalents without buildup of a charge. We find that substituting deuterium for hydrogen resulted i...

We extend the class of wavefunctions used within the framework of the Variational Quantum Eigensolver. Testing such extended variational space in simple cases, we achieve high quality wavefunction with reduced circuit depth.

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 S1<-S0 vertical transition have been computed using d...

Water oxidation in the early steps of natural photosynthesis is fulfilled by Photosystem II, a protein complex embedded in the thylakoid membrane inside chloroplasts. The water oxidation reaction occurs in the catalytic core of Photosystem II, consisting of a Mn4Ca metal cluster where, after the accumulation of four oxidizing equivalents through fi...

The binding motifs in the halide adducts with tyrosine ([Tyr+X]-, X = Cl, Br, I) have been investigated and compared with the analogues with 3-nitrotyrosine (nitroTyr), a biomarker of protein nitration, in a solvent-free environment by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy over two IR frequency ranges, namely 950-...

GabR from Bacillus subtilis is a transcriptional regulator belonging to the MocR subfamily of the GntR regulators. The structure of the MocR regulators is characterized by the presence of two domains: i) a N-terminal domain, about 60 residue long, possessing the winged-Helix-Turn-Helix (wHTH) architecture with DNA recognition and binding capability...

RMSD and RMSF variations of the wHTH domains of holo and apo GabR. RMSD and RMSF are reported in (A) and (B), respectively. Color code is indicated in the insets of the plots. Calculations have been carried out taking into account only the main chain atoms. (PDF)

Movie of the 350 ns simulation of the holo GabR form. PLP is represented by space filling models. Movie file is encoded with H.264 in an MP4 container. (MP4)

Movie of the 200 ns simulation of apo GabR. File format is as in S6 Movie. (MP4)

PDB coordinates of the holo GabR form with hydrogen added, used for molecular dynamics simulation. (PDB)

RMSD and RMSF variations of GabR with and without imidazole. RMSD and RMSF are reported in (A) and (B), respectively. Color code is indicated in the inset of the plot. Calculations have been carried out taking into account only the main chain atoms. (PDF)

RMSD variations. Plot of the RMSD over the initial conformation of the residues Arg319B (A) and Arg207B (B).versus simulation time. Black and red line traces refer to holo and apo GabR, respectively. (PDF)

PDB coordinates of the apo GabR form with hydrogen added and rebuilt loops, used for molecular dynamics simulation. (PDB)

GabR from Bacillus subtilis is a transcriptional regulator belonging to the MocR subfamily of the GntR regulators. The structure of the MocR regulators is characterized by the presence of two domains: i) a N-terminal domain, about 60 residue long, possessing the winged-Helix-Turn-Helix (wHTH) architecture with DNA recognition and binding capability...

Multi-center transition metal complexes are the key moieties of many processes in chemistry, biochemistry and materials science such as in the active sites of enzymes, molecular catalysts and biological electron carriers. Their electronic structure, often characterized by high spin-polarized metal sites, is a challenge for theoretical chemists beca...

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 S1 <- S0 vertical transition have been computed using...

Light harvesting from the Sun by antenna complexes surrounding the reaction center of Photosystem II represents the first step of the natural oxygenic photosynthesis performed by plants, algae and cyanobacteria. The excitation energy derived from the sunlight is absorbed by the chlorophylls of the antenna and subsequently conveyed to the reaction c...

The Mn4CaO5 cluster of Photosystem II promotes a crucial step in the oxygenic photosynthesis, namely, the water splitting reaction. The structure of such cluster in the S1 state of the Kok-Joliot's cycle has been recently resolved by femtosecond X-ray free electron laser (XFEL) measurements. However, the XFEL results are characterized by appreciabl...

The gas-phase structural modifications induced by the oxidation of methionine of two peptides of reverse sequence, methionine-valine (Met-Val) and valine-methionine (Val-Met), have been studied by mass-selected infrared multiple photon dissociation (IRMPD) spectroscopy in the 800-2000 cm-1 fingerprint range at the Centre Laser Infrarouge d'Orsay (C...

Electron correlation plays a crucial role in the energetics of reactions catalyzed by transition metal complexes, such as water splitting. In the present work we exploit the performance of various methods to describe the thermodynamics of a simple but representative model of water splitting reaction, based on a single cobalt ion as catalyst. Densit...

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 Br...

In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with...

Peridinin (Per) is a carbonyl-containing carotenoid playing a key role in light harvesting and photoprotection in dinoflagellates. This carotenoid plays its photoprotective role by quenching the potentially dangerous ³Chl-a triplet state through the formation of the non-reactive ³Per triplet state through Dexter energy transfer mechanism. We have i...

A detailed knowledge of the structures of the catalytic steps along the Kok-Joliot cycle of Photosystem II may help to understand the strategies adopted by this unique enzyme to achieve water oxidation. Vibrational spectroscopy has probed in the last decades the intermediate states of the catalytic cycle, although the interpretation of the data tur...

The two water molecules serving as substrate for the oxygen evolution in Photosystem II are already bound in the S2 state of the Kok-Joliot's cycle. Nevertheless, an additional water molecule is supposed to bind the cluster during the transition between the S2 and S3 states, which has been recently revealed to have the Mn4CaO5 catalytic cluster arr...

A potassium-containing hexaazamacrocyclic dication, [M•H•K]2+, is able to add in the gas phase mono- and dicarboxylate anions as well as inorganic anions by forming the corresponding monocharged adducts, the structure of which markedly depends on the basicity of the anion. With anions, such as acetate or fluoride, the neutral hexaazamacrocycle M ac...

An elusive tetrahedral hydration structure for bromide in aqueous solution has been unveiled through the use of ab initio Molecular Dynamics. It has been revealed that a subset of first shell water molecules has a preferential strong interaction with the ion lone pairs, giving rise to a tetrahedral short lived complex. Through the use of a new geom...

Cholophylls are at the basis of the photosynthetic energy conversion mechanisms in algae, plants and cyanobacteria. In Photosystem II, the photo-produced electrons leave a special pair of chlorophylls (namely PD1 and PD2) that becomes cationic. This oxidizing pair [PD1,PD2]+ in turn, triggers a cascade of oxidative events, eventually leading to wat...

An algorithm for calculating the ground state (low-spin) energy and force of a multi-center transition metal (MCTM) complexes using only single determinant broken symmetry states is formulated using Heisenberg-Dirac-van Vleck formulation of spin Hamiltonian. We considered several broken symmetry states of the Schrödinger equation using the Density...

The Mn4CaO5 cluster in the oxygen-evolving complex is the catalytic core of the Photosystem II (PSII) enzyme, responsible for the water splitting reaction in oxygenic photosynthesis. The role of the redox inactive ion in the cluster has not yet fully clarified, although several experimental data are available on Ca(2+) - depleted and Ca(2+) - subst...

Due to the crucial role played by electron correlation, the accurate determination of ground state geometries of pi-conjugated molecules is still a challenge for many quantum chemistry methods. Thanks for the high parallelism of the algorithms and their explicit treatment of electron correlation effects, Quantum Monte Carlo calculations can offer a...

Amorphous transition-metal (hydr)oxides are considered as the most promising catalysts that promote the oxidation of water to molecular oxygen, protons and "energized" electrons and, in turn, as fundamental parts of "artificial leaves", that can be exploited for large scale generation of chemical fuels (e.g., hydrogen) directly from sunlight. We pr...

Protonated Hexaazamacrocycles as Selective K+ Receptors Caterina Fraschetti,1 Antonello Filippi,1 Maria Elisa Crestoni,1 Enrico Marcantoni,2 Marco Glucini,2 Laura Guarcini,1 Maria Montagna,1 Leonardo Guidoni,3 Maurizio Speranza1 1Dipartimento di Chimica e Tecnologia del Farmaco, Università La Sapienza, Rome, Italy 2Scuola di Scienze e Tecnologie,...

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 ener...

Protonated hexaazamacrocycle [M•H]+ is able to detect K+ ions present at ppb level in methanolic solutions containing 10−5 M of Na+ ions. The high sensitivity and selectivity of [M•H]+ for K+ is ascribed to the favorable energy balance between the K+ ion desolvation and its coordination to the [M•H]+ macrocycle, which allows the formation of the co...

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, h...

We investigate the effects of the static and dynamical electronic correlations on the level of conjugation of the trans-1,3-butadiene 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...

The IRMPD spectrum of the G-quartet–Na+ complex, in combination with an ab initio molecular dynamic simulation, revealed the presence of two metastable populations of conformers separated by a free energy barrier easily accessible at room temperature.

The gas-phase ions of protonated L-glutathione as native species, [GSH+H]+, and S-nitroso derivative, [GSNO+H]+, have been generated by electrospray ionization and probed via infrared multiple photon dissociation (IRMPD) action spectroscopy. Insight into the conformational landscape is gained from the interpretation of the IR spectra aided by high-...

A large variety of Ti catalysts are involved in the polymerization of ethylene, propylene, 1,3 butadiene and other di-olefins. In the present work we deal with the reaction mechanism of Cp2TiCl2 which in combination with methylaluminoxane (MAO) as alkylating agent produces a predominantly cis-1,4 poly(butadiene) (cis content of about 80 %). Differe...

We reported here the structural and vibrational properties of anti-cancer drug cis- platin (cis-[Pt(NH3)2Cl2]) in gas phase, in solid phase and in aqueous solution using DFT calculations, QM/MM molecular dynamics and effective normal modes analysis. In contrast with the gas phase case, asymmetric hydrogen bonding environments are found in both soli...

Significance A key step in natural photosynthesis is the water-splitting reaction into molecular oxygen and hydrogen equivalents. Understanding the molecular mechanisms behind this photoreaction will unravel the secrets of solar energy conversion in biochemistry and may inspire the design of artificial biomimetic materials for green energy producti...

In the present paper, we provide an extended study of the vibrational signature of a butenolide carotenoid, peridinin, in various solvents by combining resonance Raman spectroscopy (RRS) with theoretical calculations. The presence of a Fermi resonance due to coupling between the lactonic C=O stretching and the overtone of the wagging of the C-H in...

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 t...

In this letter, we report the singlet ground state structure of the full carotenoid peridinin by means of variational Monte Carlo (VMC) calculations. The VMC relaxed geometry has an average bond length alternation of 0.1165(10) Å, larger than the values obtained by DFT (PBE, B3LYP, and CAM-B3LYP) and shorter than that calculated at the Hartree−Fock...

Diradical molecules are essential species involved in many organic and inorganic chemical reactions. The computational study of their electronic structure is often challenging, because a reliable description of the correlation, and in particular of the static one, requires multireference techniques. The Jastrow correlated antisymmetrized geminal po...

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H2, Be2, H2O, and C2H4). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions...

An important approach in the design of new environmentally friendly materials is represented by the study of analogous systems already existing in nature. In the search for new water splitting catalysts, the corresponding natural analogue is represented by the oxygen-evolving complex of photosystem II, which is a large membrane protein complex pres...

Split and polish: Quantum mechanics/molecular mechanics simulations reveal the role of spin surfaces, kinetics, and thermodynamics on the interconversion between two structural models of the {Mn4 CaO5 } cluster in the S2 state of the water-splitting Kok's cycle in photosystem II. The results account for the temperature, illumination, and procedure...

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...

Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansa...

The O-H stretching vibrational modes of water molecules are sensitive to their local environments. Here, we applied effective normal mode analysis to isolate contributions of each of the two hydrogen atoms to the vibrational modes nu(1) and nu(3) of water molecules in the liquid phase. We demonstrate that the decoupling of the two contributions f(d...

The in-depth understanding of the molecular mechanisms regulating the water oxidation catalysis is of key relevance for the rationalization and the design of efficient oxygen evolution catalysts based on earth-abundant transition metals. Performing ab initio DFT+U molecular dynamics calculations of cluster models in explicit water solution, we prov...

We review here some of the most reliable and efficient computational theoretical ab initio techniques for the prediction of optical and electronic spectroscopic properties and show some important applications to molecules, surfaces, and solids. We investigate the role of the solvent in the optical absorption spectrum of indole molecule. We study th...

Glutathione transferases (GSTs) are protection enzymes capable of conjugating glutathione (GSH) to toxic compounds. During evolution an important catalytic cysteine residue involved in GSH activation was replaced by serine or, more recently, by tyrosine. The utility of these replacements represents an enigma because they yield no improvements in th...