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In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136–146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.

Quantum chemistry offers a large variety of methods to treat excited states. Many of them are based on a multireference wave function ansatz and are therefore characterized by an intrinsic complexity and high computational costs. To overcome these drawbacks and also some limitations of simpler single-reference approaches (e.g., configuration interaction singles and time-dependent density functional theory), the single-determinant Δself-consistent field-initial maximum overlap method (ΔSCF-IMOM) has been proposed. This strategy substitutes the aufbau principle with a criterion that occupies molecular orbitals at successive SCF iterations on the basis of their maximum overlap with a proper set of guess orbitals for the target excited state. In this way, it prevents the SCF process to collapse to the ground state wave function and provides excited state single Slater determinant solutions to the SCF equations. Here, we propose to extend the applicability of the IMOM to the treatment of localized excited states of large systems. To accomplish this task, we coupled it with the QM/ELMO (quantum mechanics/extremely localized molecular orbitals) strategy, a quantum mechanical embedding method in which the most chemically relevant part of the system is treated with traditional quantum chemical approaches, while the rest is described by extremely localized molecular orbitals transferred from recently constructed libraries or proper model molecules. After presenting the theoretical foundations of the new IMOM/ELMO technique, in this paper, we will show and discuss the results of preliminary test calculations carried out on both model systems (i.e., decanoic acid, decene, decapentaene, and solvated acrolein) and a system of biological interest (flavin mononucleotide in the flavodoxin protein). We observed that, for localized excited states, the new IMOM/ELMO method provides reliable results, and it reproduces the outcomes of fully IMOM calculations within the chemical accuracy threshold (i.e., 0.043 eV) by including only a limited number of atoms in the QM region. Furthermore, the first application of our embedding technique to a larger biological system gave completely plausible results in line with those obtained through more traditional quantum mechanical methods, thus opening the possibility of using the new approach in future investigations of photobiology problems.

The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.

Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.

The development of computationally advantageous methods for the study of large systems is a long-standing research topic in theoretical chemistry. Among these techniques, a prominent place is certainly occupied by the multiscale embedding strategies, from the well-known QM/MM (quantum mechanics/molecular mechanics) methods to the latest and promising fully quantum mechanical approaches. In this Feature Article, we will briefly review the recently proposed QM/ELMO (quantum mechanics/extremely localized molecular orbital) scheme, namely a new multiscale embedding strategy in which the most chemically relevant region of the investigated system is treated at fully quantum chemical level, while the remaining part (namely, the environment) is described by means of transferred extremely localized molecular orbitals that remain frozen throughout the computation. Other than highlighting the theoretical bases, here we will also review the main results obtained through all the currently available variants of the novel method. In particular, we will show how the QM/ELMO embedding scheme has been successfully exploited to perform both ground and excited state calculations, reproducing the results of corresponding fully quantum mechanical computations but with a much lower computational cost. A first application to crystallography will be also discussed, and we will describe how the QM/ELMO approach has been recently coupled with the Hirshfeld atom refinement technique to accurately determine the positions of hydrogen atoms from X-ray diffraction data. Given the reliability and quality of the obtained results, future applications of the current versions of the QM/ELMO embedding strategy to different types of chemical problems are to be expected in the near future. Moreover, further algorithmic improvements and methodological developments are also envisaged, such as the development of a polarizable QM/ELMO scheme accounting for the effects of the QM region on the ELMO subsystem or the use of the new embedding approach in the context of quantum crystallography to perform unprecedented accurate refinements of macromolecular crystal structures.

The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water. Electron interaction cross sections for elastic scattering, ionisation, and electronic excitation were calculated in the four DNA bases adenine, thymine, guanine and cytosine. The electron energy range is extended to include relativistic electrons. Elastic scattering cross sections were calculated using the independent atom model with amplitude derived from ELSEPA code. Relativistic Binary Encounter Bethe Vriens model was used to calculate ionisation cross sections. The electronic excitation cross sections calculations were based on the water cross sections following the same strategy used in CPA100 code. These were implemented within the Geant4-DNA option6 physics constructor to extend its capability of tracking electrons in DNA material in addition to liquid water. Since DNA nucleobases have different molecular structure than water it is important to perform more accurate simulations especially because DNA is considered the most radiosensitive structure in cells. Differential and integrated cross sections calculations were in good agreement with data from the literature for all DNA bases. Stopping power, range and inelastic mean free path calculations in the four DNA bases using this new extension of Geant4-DNA option6 are in good agreement with calculations done by other studies, especially for high energy electrons. Some deviations are shown at the low electron energy range, which could be attributed to the different interaction models. Comparison with water simulations shows obvious difference which emphasizes the need to include DNA bases cross sections in track structure codes for better estimation of radiation effects on biological material., 23 pages, 12 figures, 1 table

Embedding techniques are nowadays considered the go-to-methods to have an optimal trade-off between chemical accuracy and computational cost in modeling large molecular systems. Several efficient strategies of this kind have been developed over the years, from QM/MM (quantum mechanics/molecular mechanics) techniques to more recent and promising density functional theory embedding approaches. Along this line, we have recently proposed the QM/ELMO (quantum mechanics/extremely localized molecular orbital) method. This strategy describes the chemically important region of an extended system at a fully quantum mechanical (QM) level, while the rest is treated through frozen extremely localized molecular orbitals (ELMOs) properly transferred from recently assembled libraries or ad hoc model molecules. In this work, after reviewing the theoretical bases of the novel technique, we will show and discuss the results of further validation tests, with a particular focus on basis set dependence and computational cost.

The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.

Equation-of-Motion Coupled Cluster with single and double excitations (EOM-CCSD) is currently one of the most accurate quantum chemical methods for the investigation of excited-states, but its non-negligible computational cost unfortunately limits its application to small molecules. To extend its range of applicability, one possibility consists in its coupling with the so-called multi-scale embedding techniques. Along this line, in this work we propose the interface of the EOM-CCSD method with the recently developed quantum mechanics / extremely localized molecular orbital (QM/ELMO) strategy, an approach where the chemically relevant region of the investigated system is treated at fully quantum chemical level (QM region), while the remaining part (namely, the chemical environment) is described through transferred and frozen extremely localized molecular orbitals (ELMO subsystem). In order to determine capabilities and limitations of the novel EOM-CCSD/ELMO approach, some validation tests were properly designed and carried out. They indicated that the new approach is particularly useful and efficient in describing local electronic transitions in relatively large systems, for both covalently and non-covalently bonded QM and ELMO regions. In particular, it has been shown that, including only a limited number of atoms in the chemically active subunit, the ELMO-embedded computations enable the reproduction of excitation energies and oscillator strengths resulting from full EOM-CCSD calculations within the limit of chemical accuracy, but with a significantly reduced computational cost. Furthermore, despite the approximation of an embedding potential given by frozen extremely localized molecular orbitals, it was observed that the new strategy is able to satisfactorily account for the effects of the environment.

The QM/ELMO (quantum mechanics / extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under exam is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited-states and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT). The proposed TDDFT/ELMO strategy has been subjected to a series of preliminary tests that were already considered for the validations of other embedding TDDFT methods. The obtained results show that the novel technique allows the accurate description of local excitations in large systems by only including a relatively small group of atoms in the region treated at fully quantum chemical level. Furthermore, it was observed that, even using functionals that do not take into account long-range corrections, the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations. Finally, through the application to a reduced model of the Green Fluorescent Protein, it was proved that the TDDFT/ELMO approach can be also successfully exploited to investigate local electronic transitions in large systems and that the accuracy of the results can be improved by including a sufficient number of fragments/residues that are chemically crucial in the quantum mechanical region. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical methods for excited-states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multi-references methods.

Embedding strategies currently provide the best compromise between accuracy and computational cost in modeling chemical properties and processes of large and complex systems. In this framework, different methods have been proposed all over the years, from the very popular QM/MM approaches to the more recent and very promising density matrix and density functional embedding techniques. Here, we present a further development of the quantum mechanics/extremely localized molecular orbital technique (QM/ELMO) method, a recently proposed multiscale embedding strategy in which the chemically active region of the investigated system is treated at a fully quantum mechanical level, while the rest is described by frozen extremely localized molecular orbitals previously transferred from proper libraries or tailor-made model molecules. In particular, in this work we discuss and assess in detail the extension of the QM/ELMO approach to density functional theory and post-Hartree-Fock techniques by evaluating its performances when it is used to describe chemical reactions, bond dissociations, and intermolecular interactions. The preliminary test calculations have shown that, in the investigated cases, the new embedding strategy enables the results of the corresponding fully quantum mechanical computations to be reproduced within chemical accuracy in almost all the cases but with a significantly reduced computational cost, especially when correlated post-Hartree-Fock strategies are used to describe the quantum mechanical subsystem. In light of the obtained results, we already envisage the future application of the new correlated QM/ELMO techniques to the investigation of more challenging problems, such as the modeling of enzyme catalysis, the study of excited states of biomolecules, and the refinement of macromolecular X-ray crystal structures.

Five organic salts of the antiplasmodial drug piperaquine (PQ, C 29 H 32 Cl 2 N 6 ) were synthesized and characterized by X-ray diffraction methods. The corresponding solubilities in water and acetic acid solutions were evaluated in the 20-50 °C (293-323 K) T range by UV-vis spectroscopy, with the aim of elucidating how they depend on chemical, structural, and thermodynamic factors. Experiments were complemented by DFT calculations, both in vacuo and in the solid state, to estimate changes in thermodynamic state functions related to the solvation process. It is demonstrated that solubility is mainly governed by the electronic and chemical properties of the anion, while lattice energies and packing effects, including in-crystal conformational changes of the drug, play a less important role. PQ salts generally conform to the predictions of hard and soft acid and bases (HSAB) theory, as less soluble compounds bear ions of comparable hardness, and vice versa. A remarkable exception is the PQ hydrogen sulfate salt, whose poor solubility can be ascribed to an exceptionally stable crystal lattice. Other factors, such as entropic effects related to solid-state disorder, can influence the response of solubility to temperature.

The Source Function (SF) tool was applied to the analysis of thetheoreticalspin density in azido CuIIdinuclear complexes, where the azido group, acting as a coupler between the CuIIcations, is linked to the metal centres either in an end-on or in an end–end fashion. Results for only the former structural arrangement are reported in the present paper. The SF highlights to which extent the magnetic centres contribute to determine the local spin delocalization and polarization at any point in the dimetallic complex and whether an atom or group of atoms of the ligands act in favour or against a given local spin delocalization/polarization. Ball-and-stick atomic SF percentage representations allow for a visualization of the magnetic pathways and of the specific role played by each atom along these paths, at given reference points. Decomposition of SF contributions in terms of a magnetic and of a relaxation component provides further insight. Reconstruction of partial spin densities by means of the Source Function has for the first time been introduced. At variance with the standard SF percentage representations, such reconstructions offer a simultaneous view of the sources originating from specific subsets of contributing atoms, in a selected molecular plane or in the whole space, and are therefore particularly informative. The SF tool is also used to evaluate the accuracy of the analysed spin densities. It is found that those obtained at the unrestricted B3LYP DFT level, relative to those computed at the CASSCF(6,6) level, greatly overestimate spin delocalization to the ligands, but comparatively underestimate magnetic connection (spin transmission) among atoms, along the magnetic pathways. As a consequence of its excessive spin delocalization, the UB3LYP method also overestimates spin polarization mechanisms between the paramagnetic centres and the ligands. Spin delocalization measures derived from the refinement of Polarized Neutron Diffraction data seem in general superior to those obtained through the DFT UB3LYP approach and closer to the far more accurate CASSCF results. It is also shown that a visual agreement on the spin-resolved electron densities ραand ρβderived from different approaches does not warrant a corresponding agreement between their associated spin densities.

One of the well-established methods of modern quantum crystallography is undoubtedly the X-ray constrained wavefunction (XCW) approach, a technique that enables the determination of wavefunctions which not only minimize the energy of the system under examination, but also reproduce experimental X-ray diffraction data within the limit of the experimental errors. Initially proposed in the framework of the Hartree–Fock method, the strategy has been gradually extended to other techniques of quantum chemistry, but always remaining limited to a single-determinant ansatz for the wavefunction to extract. This limitation has been recently overcome through the development of the novel X-ray constrained spin-coupled (XCSC) approach [Genoni et al. (2018). Chem. Eur. J. 24, 15507–15511] which merges the XCW philosophy with the traditional spin-coupled strategy of valence bond theory. The main advantage of this new technique is the possibility of extracting traditional chemical descriptors (e.g. resonance structure weights) compatible with the experimental diffraction measurements, without the need to introduce information a priori or perform analyses a posteriori. This paper provides a detailed theoretical derivation of the fundamental equations at the basis of the XCSC method and also introduces a further advancement of its original version, mainly consisting in the use of molecular orbitals resulting from XCW calculations at the Hartree–Fock level to describe the inactive electrons in the XCSC computations. Furthermore, extensive test calculations, which have been performed by exploiting high-resolution X-ray diffraction data for salicylic acid and by adopting different basis sets, are presented and discussed. The computational tests have shown that the new technique does not suffer from particular convergence problems. Moreover, all the XCSC calculations provided resonance structure weights, spin-coupled orbitals and global electron densities slightly different from those resulting from the corresponding unconstrained computations. These discrepancies can be ascribed to the capability of the novel strategy to capture the information intrinsically contained in the experimental data used as external constraints.

International audience; The development of methods for the quantum mechanical study of macromolecules has always been an important challenge in theoretical chemistry. Nowadays, the techniques proposed in this context can be used to investigate very large systems and can be subdivided into two main categories: fragmentation and embedding strategies. In this paper, by modifying and improving the local self-consistent field approach originally proposed for quantum mechanics/molecular mechanics techniques, we introduce the new multiscale embedding quantum mechanics/extremely localized molecular orbital (QM/ELMO) method. The new strategy enables treatment of chemically relevant regions of large biological molecules through usual methods of quantum chemistry while describing the remaining parts of the systems by means of frozen extremely localized molecular orbitals transferred from properly constructed libraries. Test calculations have shown the correct functioning and the high reliability of the new approach, thus anticipating its possible applications to different fields of physical chemistry, such as rational drug design and structural refinements of proteins.

The electron density distribution of the complex monoanion Cu(CF3)4 in (Bu4N)[Cu(CF3)4] has been studied by high-resolution X-ray single-crystal diffraction and augmented with theoretical calculations. The study finds that the central copper bears an atomic charge of close to +1, while the occupancy of its dx2-y2 orbital is only 1.26. Using topological analysis combined with theoretical calculations, the depopulation of dx2-y2 is shown to be due to significant covalency in the Cu-C bonds. The combination of the monovalent picture and the covalency is interpreted as a confirmation of an inverted ligand field.

The relevant noncovalent interaction patterns responsible for intermolecular recognition of the antiplasmodial chloroquine (CQ) in its bioactive diprotonated form, CQH(2)(2+), are investigated. Chloroquine dihydrogen phosphate hydrated salt (P2(1)/c) was crystallized by gel diffusion. A high-resolution single-crystal X-ray diffraction experiment was performed at 103(2) K, and a density functional theory model for the in-crystal electron density was derived, allowing the estimation of the interaction energies in relevant molecular pairs. H2PO4- ions form infinite chains parallel to the monoclinic axis, setting up strong NH center dot center dot center dot O charge-assisted hydrogen bonds (CAHBs) with CQH(2)(2+). Couples of facing protonated quinoline rings are packed in a pi center dot center dot center dot pi stacked arrangement, whose contribution to the interaction energy is very low in the crystal and completely overwhelmed by Coulomb repulsion between positive aromatic rings. This questions the ability of CQ in setting up similar stacking interactions with the positively charged Fe-protoporphyrin moiety of the heme substrate in solution. When the heme/CQ adduct incorporates a FeN coordinative bond, stronger pi center dot center dot center dot pi interactions are instead established due to the lacking of net electrostatic repulsions. Yet, CAHBs among the protonated tertiary amine of CQ and the propionate group of heme still provide the leading stabilizing effect. Implications on possible modifications/improvements of the CQ pharmacophore are discussed.

Hirshfeld atom refinement (HAR) is a method for refining X-ray crystal structures that is able to provide bond lengths involving hydrogen atoms in statistical agreement with those derived from neutron diffraction data, provided the data reach 0.8 A resolution. Rather than using tabulated spherical atomic structure factors, HAR uses “tailor made” aspherical atomic structure factors obtained directly from quantum chemical calculations. Despite the very good results obtained so far, which make HAR an emerging refinement method of modern crystallography, until now all the Hirshfeld atom refinements were exclusively based on Hartree-Fock (HF) or density functional theory (DFT) methods, but never on the so-called post-HF techniques of quantum chemistry. Post-HF methods exploit more sophisticated multi-determinant wavefunctions and, consequently, should provide more accurate electron densities for the refinements. For this reason, for the first time we have performed HARs based on two well-known post-HF strategies (MP2 and Coupled Cluster) combined with three different basis-sets (def2-SVP, def2-TZVP and def2-TZVPP). The obtained results have been afterwards analyzed and compared to those resulting from neutron and other Hirshfeld atom refinements, the latter relying on Hartree-Fock and DFT (BLYP and B3LYP) calculations in order to evaluate if the use of more sophisticated and expensive approaches of quantum chemistry can improve the performances of the HAR technique.

The electron density distribution of the complex monoanion Cu(CF

Thorough searches for more and more performing materials or for materials with novel properties and functions require a profound understanding of their structure-property relationships. While a detailed knowledge of the structure of a material, either through experimental and/or in silico ap- proaches, is a necessary and fundamental prerequisite for its study, it should not be overlooked that the geometrical and electronic (and magnetic) structure of a material is ultimately related to its chemical bonding features. And as an obvious consequence, the material's properties are in turn de- termined by those same features. The aim of this chapter is therefore to present an overview of theories, models and techniques which have found broad applications in the study of chemical bonding in materials. Rather than offering a comprehensive list of examples from literature, our main focus is on discussing the basic tenets of such tools, along with a discussion of their physical contents and limits, so as to favor their proper use. None- theless, the chapter concludes with a number of worked examples, illus- trating in some detail the synergic use of most of the outlined approaches.

Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4

4-aminoquinoline antiplasmodials interfere with the biocrystallization of the malaria pigment, a key step of the malaria parasite metabolism. It is commonly believed that these drugs set stacking pi center dot center dot center dot pi interactions with the Fe-protoporphyrin scaffold of the free heme, even though the details of the heme: drug recognition process remain elusive. In this work, the local coordination of Fe(III) ions in acidic solutions of hematin at room temperature was investigated by extended x-ray absorption fine structure (EXAFS) spectroscopy in the 4.0-5.5 pH range, both in the presence and in the absence of the antimalarial drug chloroquine. EXAFS results were complemented by DFT simulations in polarizable continuum media to model solvent effects. We found evidence that a complex where the drug quinoline nitrogen is coordinated with the iron center might coexist with formerly proposed adduct geometries, based on stacking interactions. Charge-assisted hydrogen bonds among lateral chains of the two molecules play a crucial role in stabilizing this complex, whose formation is favored by the presence of lipid micelles. The direct Fe-N bond could reversibly block the axial position in the Fe 1st coordination shell in free heme, acting as an inhibitor for the crystallization of the malaria pigment without permanently hampering the catalytic activity of the redox center. These findings are discussed in the light of possible implications on the engineering of drugs able to thwart the adaptability of the malaria parasite against classical aminoquinoline-based therapies.

Malaria is one of the most worldwide spread parasitic disease. It is caused by Plasmodium protozoa, which eventually infect human erythrocytes and digest the host haemoglobin. This process releases free haeme (Fe-protoporphyrin-IX), which is toxic to the parasite as it produces reactive oxygen species (ROS), the cause of oxidative stress. The protozoon deactivates haeme by promoting its crystallization into solid pale-yellow hemozoin, that gives the characteristic skin color of malaria-infected people. Aminoquinoline-type (AQ) drugs interfere with this detoxification process either by directly hampering haeme-haeme self-recognition in solution [ ] or by preventing the growth of hemozoin crystals [ ] (Figure 1). The nature of the specific AQ compound-haeme scaffold interactions is not yet understood, even though it is a necessary requirement to explicate antiplasmodial activity. We report here on an experimental and theoretical study of the AQ- type antimalarial chloroquine (CQ)-free haeme interactions in aqueous solutions. Extended X-ray Absorption Fine Structure (EXAFS) experiments at the Fe Kalgfa absorption edge (7.1 keV) were performed at the BM26A station of the ESRF facility in Grenoble (FR) on various haeme-containing solutions, both in the presence and in the absence of CQ. The effect of pH was monitored through the addition of suitable buffers in the 4-7 range at variable pH interval. A tensioactive (sodium dodecyl sulfate) at its critical micellar concentration was also employed to model lipidic nanodroplets in the parasite food vacuole, as their presence was reported [ ] to favor hemozoin crystallization (Figure 1). EXAFS results were complemented by accurate UV absorption measurements of the same solutions and DFT B3LYP 6-311G(d,p) simulations of possible haeme:chloroquine adduct geometries. We found evidence that, at least in the experimental conditions here employed, CQ does not set stacking pi···pi interactions with the protoporphyrin scaffold, even though this geometry was proposed as the most probable one through molecular mechanics simulations [ , ] and previous EXAFS studies of mesohaematin anhydride in dimethylsulfoxyde [ ]. Rather, our DFT calculations point out that CQ and haeme seem to recognize each other through electrostatic interactions among lateral charged groups. If proven true, this would have obvious implications on the engineering of novel antimalarials able to thwart the parasite adaptability against classical AQ-based therapies.