A new study of the  sigmaA parameter has been undertaken to understand itsbehaviour when the diffraction amplitude distributions are far from the standardWilson distributions. The study has led to the formulation of a new statisticalinterpretation of  sigmaA, expressed in terms of a correlation factor. The newformulas allow a more accurate use of  sigmaA in electron-density modification procedures.

Difference electron densities do not play a central role in modern phase refinement approaches, essentially because of the explosive success of the EDM (electron-density modification) techniques, mainly based on observed electron-density syntheses. Difference densities however have been recently rediscovered in connection with the VLD (Vive la Difference) approach, because they are a strong support for strengthening EDM approaches and for ab initio crystal structure solution. In this paper the properties of the most documented difference electron densities, here denoted as F - F p, mF - F p and mF - DF p syntheses, are studied. In addition, a fourth new difference synthesis, here denoted as synthesis, is proposed. It comes from the study of the same joint probability distribution function from which the VLD approach arose. The properties of the syntheses are studied and compared with those of the other three syntheses. The results suggest that the difference may be a useful tool for making modern phase refinement procedures more efficient.

The difference electron density has recently been revisited via the method ofjoint probability distribution functions [Burla et al. (2010). Acta Cryst. A66, 347-361]. New Fourier coefficients were devised which were the basis of a new abinitio method for the solution of the phase problem (i.e. VLD, vive la difference).In this paper we study the joint probability distribution functions P(F, Fp, Fq),where Fq is the structure factor corresponding to the ideal hybrid Fouriersynthesis rhoq =  trho -wrhop and t and w are any pair of real numbers. New Fouriercoefficients for the calculations of any hybrid synthesis are obtained, and theproperties of the corresponding electron-density maps are discussed. The firstapplications show the correctness of our theoretical approach and suggestpossible applications in phasing procedures.

New methods have been recently developed to improve the structure solution of macromolecules by ab initio (Patterson or Direct Methods) and non ab initio (Molecular Replacement) approaches. Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. The combined use of different algorithms [Patterson deconvolution and superposition techniques, cross-correlation function (C-Map), the VLD (Vive la Difference) approach included in the Direct Space Refinement (DSR) procedure, a new probabilistic formula estimating triplet invariants and capable of exploiting a model electron density maps, the FREE LUCH extrapolation method, a new FOM to identify the correct solution] allow to overcome the lack of experimental information. The new methods have been applied to a large number of protein diffraction data with resolution up to 2.1Å, under the condition that Ca or heavier atoms are in the structure. Results show that solving proteins at limited resolution is a feasible task, achievable even by new Direct Methods algorithms, against the traditional common believe that atomic resolution is a necessary condition for the success of a direct ab initio phasing process.A new procedure (REVAN) , aiming at solving protein structures via Molecular Replacement and density guided optimization algorithms, has been assembled. It combines a variety of programs (REMO09, REFMAC, COOT) and algorithms (Cowtan-EDM, DSR, VLD, FREE LUNCH), and can successfully lead to the structure solution also when the sequence identity between target and model structures is smaller than 0.30 and data resolution up to ~ 3Å. The application to a wide set of test structures (including difficult cases proposed by DiMaio et al. (2011), solved by using MR procedures together with energy guided programs) suggests that REVAN is quite effective even far from atomic resolution and, in combination with EDM techniques and sequence mutation algorithms, it is able to efficiently extend and refine the set of phases, reducing its average error.The final step of the automatic solving process (ab initio or MR approaches) is the application of an Automated Model Building program (i.e. Buccaneer, Nautilus, ARP-wARP or Phenix-Autobuild) in order to recover the correct structure. Results suggest that the quality of the phases at the end of the phasing process is good enough to lead the AMB program to success.These new efficient procedures are implemented in the current version of the software package SIR2014.

New methods have been recently developed to improve the structure solution of macromolecules by ab initio (Patterson or Direct Methods) and non ab initio (Molecular Replacement) approaches. Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. The combined use of different algorithms [Patterson deconvolution and superposition techniques, cross-correlation function (C-Map), the VLD (Vive la Difference) approach included in the Direct Space Refinement (DSR) procedure, a new probabilistic formula estimating triplet invariants and capable of exploiting a model electron density maps, the FREE LUCH extrapolation method, a new FOM to identify the correct solution] allow to overcome the lack of experimental information. The new methods have been applied to a large number of protein diffraction data with resolution up to 2.1Å, under the condition that Ca or heavier atoms are in the structure. Results show that solving proteins at limited resolution is a feasible task, achievable even by new Direct Methods algorithms, against the traditional common believe that atomic resolution is a necessary condition for the success of a direct ab initio phasing process. A new procedure (REVAN) , aiming at solving protein structures via Molecular Replacement and density guided optimization algorithms, has been assembled. It combines a variety of programs (REMO09, REFMAC, COOT) and algorithms (Cowtan-EDM, DSR, VLD, FREE LUNCH), and can successfully lead to the structure solution also when the sequence identity between target and model structures is smaller than 0.30 and data resolution up to ~ 3Å. The application to a wide set of test structures (including difficult cases proposed by DiMaio et al. (2011), solved by using MR procedures together with energy guided programs) suggests that REVAN is quite effective even far from atomic resolution and, in combination with EDM techniques and sequence mutation algorithms, it is able to efficiently extend and refine the set of phases, reducing its average error. The final step of the automatic solving process (ab initio or MR approaches) is the application of an Automated Model Building program (i.e. Buccaneer, Nautilus, ARP-wARP or Phenix-Autobuild) in order to recover the correct structure. Results suggest that the quality of the phases at the end of the phasing process is good enough to lead the AMB program to success. These new efficient procedures are implemented in the current version of the software package SIR2014.

The REVAN pipeline aiming at the solution of protein structures via molecular replacement (MR) has been assembled. It is the successor to REVA, a pipeline that is particularly efficient when the sequence identity (SI) between the target and the model is greater than 0.30. The REVAN and REVA procedures coincide when the SI is >0.30, but differ substantially in worse conditions. To treat these cases, REVAN combines a variety of programs and algorithms (REMO09, REFMAC, DM, DSR, VLD, free lunch, Coot, Buccaneer and phenix. autobuild). The MR model, suitably rotated and positioned, is first refined by a standard REFMAC refinement procedure, and the corresponding electron density is then submitted to cycles of DM-VLD-REFMAC. The next REFMAC applications exploit the better electron densities obtained at the end of the VLD-EDM sections (a procedure called vector refinement). In order to make the model more similar to the target, the model is submitted to mutations, in which Coot plays a basic role, and it is then cyclically resubmitted to REFMAC-EDM-VLD cycles. The phases thus obtained are submitted to free lunch and allow most of the test structures studied by DiMaio et al. [(2011), Nature (London), 473, 540-543] to be solved without using energy-guided programs.

The VLD algorithm relies on the properties of the difference Fourier synthesisand is designed for solving crystal structures in the correct space group, startingfrom random models. The standard approach has been modified by integrating itwith the RELAX procedure, for translating to the correct position misplacedbut correctly oriented models. A better control of the parameters and additionalphase refinement cycles were able to improve the quality of the solutions and tomake superfluous, for macromolecules and medium-sized molecules, the least-squares refinement cycles that, in the standard VLD approach, follow thephasing step. As a result, the efficiency of the new VLD algorithm is stronglyincreased; it has been checked using a wide variety of practical cases andcompared with the effectiveness of direct methods.

The identification of the extinction symbol is routine for single-crystal X-raydata. Because of peak overlap and possible preferred orientation the task ismore difficult for powder diffraction data, but recent computer programs basedon probabilistic approaches have made it more automatic. This paper describesa new algorithm for the automatic identification of the Laue group and of theextinction symbol from electron diffraction intensities. The algorithm has astatistical basis and tries to deal with the severe problems arising from the oftennonkinematical nature of the diffraction intensities and from the limitedaccuracy of the lattice parameters determined via electron diffraction. Theapproach has been checked using a wide set of test structures.

Gold nanoparticles exhibit unique electronic, optical, and catalytic properties that are different from those of bulk metal and have several applications in optoelectronics, imaging technology, catalysis, and drug delivery. Currently, there is a growing need to develop eco-friendly nanoparticle synthesis processes using living organisms, such as bacteria, fungi and algae. In particular, microorganisms are well known to protect themselves from metal ion stress either by intracellular-segregation mechanism or by secreting them into the external medium. This defensive behaviour can be exploited to obtain a more efficient fabrication of advanced functional nanomaterials than chemical synthesis routes: biological syntheses do not require hazardous organic solvents and surfactants , and can work at environmental temperature and pressure, preserving high selectivity and reproducibility.Rhodobacter sphaeroides is a facultative phototrophic anoxygenic proteobacterium known for its capacity to grow under a wide range of environmental conditions, with promising applications in bioremediation [1, 2].The response of the photosynthetic bacterium Rhodobacter sphaeroides to gold exposure and its reducing capability of Au(III) to produce stable Au(0) nanoparticles is reported in this study. The properties of prepared nanoparticles were characterized by UV-Visible (UV-Vis) spectroscopy, Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy, Transmission Electron Microscopy (TEM), X-ray Photoelectron Spectroscopy (XPS), X-ray Fluorescence Spectrometry (XRF) and X-ray Absorption Spectroscopy (XAS) measurements. Gold nanoparticles (AuNPs) were spherical in shape with an average size of 10±3 nm. Based on our experiments, the particles were likely fabricated by the aid of reducing sugars present in the bacterial cell membrane and were capped by a protein/peptide coat. The nanoparticles were hydrophilic and resisted to aggregation for several months. Gold nanoparticles were also positively tested for their catalytic activity in nitroaromatic compounds degradation.

Cobalt is an important oligoelement required for bacteria; if present in high concentration, exhibits toxic effects that, depending on the microor-ganism under investigation, may even result in growth inhibition. The photosynthetic bacterium Rhodobacter (R.) sphaeroides tolerates high cobalt concentration and bioaccumulates Co+2 ion, mostly on the cellular surface. Very little is known on the chemical fate of the bioaccumulated cobalt, thus an X-ray absorption spectroscopy investigation was conducted on R. sphaeroides cells to gain structural insights into the Co+2 binding to cellular components. X-ray absorption near-edge spectroscopy and extended X-ray absorption fine structure measurements were performed on R. sphaeroides samples containing whole cells and cell-free fractions obtained from cultures exposed to 5 mM Co+2. An octahedral coordination geometry was found for the cobalt ion, with six oxygen-ligand atoms in the first shell. In the soluble portion of the cell, cobalt was found bound to carboxylate groups, while a mixed pattern containing equivalent amount of two sulfur and two carbon atoms was found in the cell envelope fraction, suggesting the presence of carboxylate and sulfonate metal-binding functional groups, the latter arising from sulfolipids ofthe cell envelope.

SIR2014 is the latest program of the SIR suite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (standard or modern direct methods, Patterson techniques, Vive la Différence) and non-ab initio (simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via suitable viewers.

The statistical features of the amplitudes obtained via precession electron diffraction have been studied,with particular concern with their effects on direct phasing procedures. A new algorithm, denoted by BEA,is described: according to it, the average amplitude of the symmetry equivalent reflections is used in the Direct Methods step. Once an even imperfect structural model is available, the best amplitude among theequivalent reflections is used to improve the model. It is shown that BEA is able to provide more complete structural models, to make the phasing process more straightforward and to end with crystallographicresidual much better than those usually obtained by electron diffraction.

The triplet structure invariant is estimated via the method of joint probability distribution functions when a model structure is available. The six-variate probability distribution function P(Eh, Ek, E-h-k, Eph, Epk, Ep,-h-k) is studied under the condition that imperfect isomorphism between the target and model structures exist. The results are compared with those available in the literature, which were obtained under the condition of perfect isomorphism. It is shown that the new formalism is more suitable for real cases, where perfect isomorphism is very rare.

The crystal structure solution of small-medium size molecules via single crystal X-ray data is almost a routineprocess. When single crystals of sufficient dimensions are not available, electron diffraction is a usefulalternative: the structure solution however may still be a challenge. We have modified the standard version ofSir2008 to include several new tools, which are expected to make the phasing process more straightforward.Additional work is in progress: in Sir2011, the heir of Sir2008, particular emphasis will be given to a newprocedure for the determination of the space groups, to a new approach (BEA) aiming at reducing in thepractice the disturbing effects of the dynamical scattering and to the simulated annealing algorithm, as aphasing tool particularly useful in case of organic structures, when scarce or poor experimental data areavailable.

Biological processes using microorganisms for nanoparticle synthesis are appealing as eco-friendly nanofac-tories. The response of the photosynthetic bacterium Rhodobacter sphaeroides to gold exposure and its reducingcapability of Au(III) to produce stable gold nanoparticles (AuNPs), using metabolically active bacteria andquiescent biomass, is reported in this study.In the former case, bacterial cells were grown in presence of gold chloride at physiological pH. Gold exposurewas found to cause a significant increase of the lag-phase duration at concentrations higher than 10 ?M, sug-gesting the involvement of a resistance mechanism activated by Au(III). Transmission Electron Microscopy(TEM) and Scanning Electron Microscopy/Energy Dispersive X-ray Spectrometry (SEM/EDS) analysis of bac-terial cells confirmed the extracellular formation of AuNPs.Further studies were carried out on metabolically quiescent biomass incubated with gold chloride solution.The biosynthesized AuNPs were spherical in shape with an average size of 10 ± 3 nm, as analysed byTransmission Electron Microscopy (TEM). The nanoparticles were hydrophilic and stable against aggregation forseveral months.In order to identify the functional groups responsible for the reduction and stabilization of nanoparticles,AuNPs were analysed by Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy, X-ray Photoelectron Spectroscopy (XPS), X-ray Fluorescence Spectrometry (XRF) and X-ray AbsorptionSpectroscopy (XAS) measurements. The obtained results indicate that gold ions bind to functional groups of cellmembrane and are subsequently reduced by reducing sugars to gold nanoparticles and capped by a protein/peptide coat.Gold nanoparticles demonstrated to be efficient homogeneous catalysts in the degradation of nitroaromaticcompounds.

A new probabilistic formula estimating triplet invariants [1], and capable of exploiting, as prior information, a model electron density map which is gradually created during the ab initio phasing process, has been recently tested on a set of protein structures with data at non atomic resolution [2]. All the test structures contain heavy atom larger than Ca, and show a structural complexity which may attain the value of about 8000 non-hydrogen atoms in the asymmetric unit: their data resolution varies in the interval (1.5, 2.1 Å). It has been shown that most of such structures were solved by our new Direct Methods procedure MDM [3], against the traditional common believe that atomic resolution is a necessary ingredient for the success of direct ab initio phasing. The aim of this work is to refine and to solve those test structures for which MDM was not able to provide sufficiently good models. The new technique involves the massive use of three supplementary tools: a)the so called hybrid (1-2)-Fourier synthesis ?Q = ? - 2?p according to the theory described by [4]. b)the VLD (Vive La Difference) algorithm [5] [6] [7] [8];c)the Free Lunch algorithm [9] [10].We show that most of the structures resistant to MDM are now solved by such combined procedure .[1] M.C. Burla, B. Carrozzini, G.L. Cascarano, G. Comunale, C. Giacovazzo, A. Mazzone, G. Polidori, (2012), Acta. Cryst. A68, 513-520. [2] M.C. Burla, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, G. Polidori, (2015), J. Appl. Cryst. 48, 1692-1698.[3] M.C. Burla, C. Giacovazzo, G. Polidori, (2013), J. Appl. Cryst. 46,1592-1602. [4] M.C. Burla, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, G. Polidori, (2011), Acta Cryst. A67,447-455.[5 M.C. Burla, R. Caliandro, C. Giacovazzo, G. Polidori, (2010) Acta Cryst. A66, 347-361. [6] M.C. Burla, C. Giacovazzo, G. Polidori, (2010), J. Appl. Cryst. 43,825-836. [7] M.C. Burla, C. Giacovazzo, G. Polidori, (2011), J. Appl. Cryst. 44,193-199.[8] M.C. Burla,R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Giacovazzo, G. Polidori (2011), J. Appl. Cryst. 44,1143-1151 [9] R. Caliandro, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, D. Siliqi, (2005) Acta Cryst. D61, 556-565.[10] R. Caliandro, B. Carrozzini, G.L. Cascarano, L. De Caro, C. Giacovazzo, D. Siliqi, (2005) Acta Cryst. D61, 1080-1087.

The efficient multipurpose figure of merit MPF has been defined andcharacterized. It may be very helpful in phasing procedures. Indeed, it mightbe used for establishing the centric or acentric nature of an unknown structure,for identifying the presence of some pseudotranslational symmetry, forrecognizing the correct solution in multisolution approaches and for estimatingthe quality of structure models as they become available during the phasingprocess. Thus, phase improvement or deterioration may be monitored anduseless models may be discarded to save computing time. It is also shown thatMPF may be applied in different phasing approaches, no matter if ab initio ornon ab initio.

Two new computational methods dedicated to neutron crystallography, called n-FreeLunch and DNDM-NDM, have been developed and successfully tested. The aim in developing these methods is to determine hydrogen and deuterium positions in macromolecular structures by using information from neutron density maps. Of particular interest is resolving cases in which the geometrically predicted hydrogen or deuterium positions are ambiguous. The methods are an evolution of approaches that are already applied in X-ray crystallography: extrapolation beyond the observed resolution (known as the FreeLunch procedure) and a difference electron-density modification (DEDM) technique combined with the electron-density modification (EDM) tool (known as DEDM-EDM). It is shown that the two methods are complementary to each other and are effective in finding the positions of H and D atoms in neutron density maps.

Density modification is a general standard technique which may be used to improve electron density derived from experimental phasing and also to refine densities obtained by ab initio approaches. Here, a novel method to expand density modification is presented, termed the Phantom derivative technique, which is based on non-existent structure factors and is of particular interest in molecular replacement. The Phantom derivative approach uses randomly generated ancil structures with the same unit cell as the target structure to create non-existent derivatives of the target structure, called phantom derivatives, which may be used for ab initio phasing or for refining the available target structure model. In this paper, it is supposed that a model electron density is available: it is shown that ancil structures related to the target obtained by shifting the target by origin-permissible translations may be employed to refine model phases. The method enlarges the concept of the ancil, is as efficient as the canonical approach using random ancils and significantly reduces the CPU refinement time. The results from many real test cases show that the proposed methods can substantially improve the quality of electron-density maps from molecular-replacement-based phases.

Crystallographic least-squares techniques, the main tool for crystal structure refinement of small and medium-size molecules, are for the first time used for ab initio phasing. It is shown that the chief obstacle to such use, the least-squares severe convergence limits, may be overcome by a multi-solution procedure able to progressively recognize and discard model atoms in false positions and to include in the current model new atoms sufficiently close to correct positions. The applications show that the least-squares procedure is able to solve many small structures without the use of important ancillary tools: e.g. no electron-density map is calculated as a support for the least-squares procedure.Crystallographic least-squares techniques, a fundamental tool for crystal structure refinement, are used for the first time for ab initio crystal structure solution. No help was needed from other phasing techniques, such as the calculation of electron-density maps.

The method of the joint probability distribution function was applied in order to estimate the normal structure factor amplitudes of the anomalous scatterer substructure in a FEL experiment. The two-wavelength case was examined. In this, the prior knowledge of the moduli vertical bar F-1(+)vertical bar, vertical bar F-1(-)vertical bar, vertical bar F-2(+)vertical bar, vertical bar F-2(-)vertical bar was used to predict the value of vertical bar F-oa vertical bar, which is the structure factor amplitude arising from the normal scattering of the heavy atom anomalous scatterers. The mathematical treatment provides a solid theoretical basis for the RIP (Radiation-damage Induced Phasing) method, which was originally proposed in order to take the radiation damage induced by synchrotron radiation sources into account. This was further adapted to exploit FEL data, where the crystal damage is usually more massive.

Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (C map), the VLD (vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and the free lunch extrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use of ARP/wARP to check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures: e.g. the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version of SIR2014. © 2014 International Union of Crystallography.

The Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques.

SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small- and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e. g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes three-dimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

Direct methods can be used to solve proteins of great structural complexity even when diffraction data are at non-atomic resolution. However, one of the main obstacles to the wider application of direct methods is that they reliably phase only a small fraction of the observed reflections, those with a sufficiently large value of the normalized structure factor amplitude. The subsequent phase expansion and refinement required for full structure solution are difficult. Here a new phase refinement procedure is described, which combines (1-2) difference Fourier synthesis with electron density modification techniques and the vive la difference and Free Lunch algorithms. This procedure is able to solve data resistant to other direct space refinement procedures.

A new probabilistic formula estimating triplet invariants and capable of exploiting a model electron-density map gradually created during the ab initio phasing process has been tested on a set of protein structures with data at non-atomic resolution. All the structures contain heavy atoms larger than Ca, and show a structural complexity which may attain the level of about 8000 non-hydrogen atoms in the asymmetric unit. It is shown that the majority of such structures may be solved by our direct methods procedure, which, in combination with a number of ancillary phasing tools, weakens the traditional expectation that atomic resolution is a necessary ingredient for the success of a direct ab initio phasing.

When a model structure, and more generally a model electron density rho(M)(r), is available, its cross-correlation function C(u) with the unknown true structure rho(r) cannot be exactly calculated. A useful approximation of C(u) is obtained by replacing exp[i(phi(h) - phi(Mh))] by its expected value. In this case C'(u), a potentially useful approximation of the function C(u), is obtained. In this paper the main crystallographic properties of the functions C(u) and C'(u) are established. It is also shown that such functions may be useful for the success of the phasing process.

The SIR (Semi-Invariants Representation) package has been developed for solving crystalstructures by a variety of matematical approaches (Direct and Patterson Methods, VLD, DirectSpace Methods, Molecular Rplacement).The present release of the program [1}, Sir2014 (v. 17.01) is designed to solve ab initio moleculesof different size and complexity, up to proteins, provided that data resolution is no lower than 2.0Å. Data can be collected using X-Ray or electron sources.The program can also be applied to Molecular Replacement problems, providing a powerfulpipeline to solve and refine protein structures. New features and a new Graphical User Interfacewill be shown.The program is available at the web site: http://www.ba.ic.cnr.it/softwareic/sir2014/[1] M.C. Burla, R. Caliandro, B. Carrozzini, G.L. Cascarano, C. Cuocci, C. Giacovazzo, M. Mallamo, A.Mazzone, G. Polidori Jour. Appl. Cryst., 2015, 48, 306-309.

VLD (vive la difference) is a novel ab initio phasing approachthat is able to drive random phases to the correct values. Ithas been applied to small, medium and protein structuresprovided that the data resolution was atomic. It has neverbeen used for non-ab initio cases in which some phaseinformation is available but the data resolution is usually very ?far from 1 A. In this paper, the potential of VLD is tested forthe first time for a classical non-ab initio problem: molecularreplacement. Good preliminary experimental results encour-aged the construction of a pipeline for leading partialmolecular-replacement models with errors to refined solutionsin a fully automated way. The pipeline moduli and theirinteraction are described, together with applications to a wideset of test cases.

Platinum complexes bearing phosphane ligands in cis configuration with deprotonated flavonoids (3-hydroxyflavone, quercetin) and deprotonated ethyl gallate were synthesized starting from cis-[PtCl2(PPh3)(2)]. In all cases, O,O' chelate structures were obtained. While quercetin and ethyl gallate complexes are quite stable in solution, the 3-hydroxyflavonate complex undergoes a slow aerobic photodegradation in solution with formation of salicylic and benzoic acids. The X-ray diffraction structures of quercetin and ethyl gallate complexes are reported. Cell cycle studies (in the dark) of the complexes in two human cell lines revealed that the cytotoxic activity of the complex bearing 3-hydroxyflavonate is higher than those exhibited by 3-hydroxyflavone or by cis[PtCl2(PPh3)2] alone. Density functional theory studies on the hydrolysis pathway for the 3-hydroxyflavone and ethyl gallate complexes explained the different cytotoxic activity observed for the two compounds on the basis of the different intermediates formed during hydrolysis (relatively inert hydroxy Pt complexes for ethyl gal late and monoaqua complexes for 3-hydroxyflavone). (C) 2016 Elsevier Inc All rights reserved.

The VLD (vive la difference) phasing algorithm combines the model electrondensity with the difference electron density via reciprocal space relationships toobtain new phase values and drive them to the correct values. The process isiterative and has been applied to small and medium-size structures and toproteins. Hybrid Fourier syntheses show properties that are intermediatebetween those of the observed synthesis (whose peaks should correspond to themost probable atomic positions) and those of the difference synthesis (whosepositive and negative peaks should correspond to missed atomic positions and tofalse atoms of the model, respectively). Thanks to these properties some hybridsyntheses can be used in the phase extension and refinement step, to reduce themodel bias and more rapidly move to the target structure. They have beenrecently revisited via the method of joint probability distribution functions[Burla, Carrozzini, Cascarano, Giacovazzo & Polidori (2011). Acta. Cryst. A67,447-455]. The results suggested that VLD could be usefully combined, for abinitio phasing, with the hybrid rather than with the difference Fourier synthesis.This paper explores the feasibility of such a combination and shows that theoriginal VLD algorithm is only one of several variants, all with relevant phasingcapacity. The study explores the role of several parameters in order to design astandard procedure with optimized phasing power.