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An in-depth analysis of the description of bonding within Cp'''Ni-cyclo-P 3 (Cp'''=1,2,4-tri-tert-butylcyclopentadienyl, [Ni]P 3 ) employing X-ray diffraction based multipolar modeling, density functional theory (DFT) as well as an "experimental wavefunction" obtained from X-ray restrained wavefunction (XRW) fitting is presented. The results are compared to DFT calculations on white phosphorus - an isolobal analogue to [Ni]P 3 . A complementary bonding analysis shows insights into the reactivity of [Ni]P 3 . The isolobal principle is reflected in every aspect of our analysis and the employed methods seamlessly predict the differences in reactivity of [Ni]P 3 and P 4 . Crystallographic modeling, solid-state NMR, and DFT calculations describe the dynamic behavior of the cyclo-P 3 unit in the title molecule., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

The title compound, [Fe(C 2 N 3 ) 2 (C 8 H 7 N 5 ) 2 ]·2H 2 O, has been synthesized solvothermally and characterized by single-crystal X-ray diffraction. The octa-hedral iron coordination polyhedron contains two di(pyrimidin-2-yl)amine ligands coordinated in a bidentate fashion, and two monodentate dicyanimido ligands, each coordinated via a terminal N atom, with the latter in a cis orientation. The ligand configuration about the iron atom is chiral, although the compound crystallizes as a racemic mixture: the Fe-N distances (> 2.07 Å) are characteristic of high-spin iron(II). In the crystal, an extensive series of N-H⋯N, O-H⋯N and O-H⋯O hydrogen bonds links the independent mol-ecular components into a three-dimensional framework. The H atoms of both water mol-ecules are disordered. The structure also features some π-π and anion-π inter-actions. The inter-molecular inter-actions were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots. Comparisons are made with some related compounds., (© Saadallah et al. 2023.)

Hirshfeld surface analysis is a widely used tool for identifying the types of intermolecular contacts that contribute most significantly to crystal packing stabilization. One useful metric for analyzing these contacts is the contact enrichment descriptor, which indicates the types of contacts that are over- or under-represented. In this statistical study, enrichment ratios were combined with electrostatic energy (E elec ) data for a variety of compound families. To compute the electrostatic interaction energy between atoms, charge density models from the ELMAM2 database of multipolar atoms were used. As expected, strong hydrogen bonds such as O/N-H...N and O/N-H...O typically display large enrichment values and have the most negative (i.e. favorable) electrostatic energies. Conversely, contacts that are repulsive from an electrostatic perspective are usually the most under-represented. Analyzing the enrichment ratio and electrostatic energy indicators was shown to help identify which favorable contacts are the most competitive with each other. For weaker interactions, such as hydrophobic contacts, the behavior is less clear cut and can depend on other factors such as the chemical content of the molecule. The anticorrelation between contact enrichment and E elec is generally lost for weaker contacts. However, we observed that C...C contacts are often enriched in crystal structures containing heterocycles, despite the low electrostatic attraction. For molecules with only weak hydrogen bond donors/acceptors and hydrophobic groups, the correlation between contact enrichment and E elec is still evident for the strongest of these interactions. However, there are some exceptions where the most favorable contacts from an electrostatic perspective are not the most over-represented. This can occur in cases where the shape of the molecule is complex or elongated, favoring dispersion forces and shape complementarity in the packing., (open access.)

Neuropilin 1 (NRP1), a cell-surface co-receptor of a number of growth factors and other signaling molecules, has long been the focus of attention due to its association with the development and the progression of several types of cancer. For example, the KDKPPR peptide has recently been combined with a photosensitizer and a contrast agent to bind NRP1 for the detection and treatment by photodynamic therapy of glioblastoma, an aggressive brain cancer. The main therapeutic target is a pocket of the fragment b1 of NRP1 (NRP1-b1), in which vascular endothelial growth factors (VEGFs) bind. In the crystal packing of native human NRP1-b1, the VEGF-binding site is obstructed by a crystallographic symmetry neighbor protein, which prevents the binding of ligands. Six charged amino acids located at the protein surface were mutated to allow the protein to form a new crystal packing. The structure of the mutated fragment b1 complexed with the KDKPPR peptide was determined by X-ray crystallography. The variant crystallized in a new crystal form with the VEGF-binding cleft exposed to the solvent and, as expected, filled by the C-terminal moiety of the peptide. The atomic interactions were analyzed using new approaches based on a multipolar electron density model. Among other things, these methods indicated the role played by Asp320 and Glu348 in the electrostatic steering of the ligand in its binding site. Molecular dynamics simulations were carried out to further analyze the peptide binding and motion of the wild-type and mutant proteins. The simulations revealed that specific loops interacting with the peptide exhibited mobility in both the unbound and bound forms.

This article reports a practical synthesis of tert -butyl acetyl-carbamate, C 7 H 13 NO 3 , from N -Boc-thio-acetamide and the study of its crystal structure. The reaction proceeds in the presence of natural phosphate as a catalyst, with excellent yield, simple workup and benign environment. The crystal structure was refined using a transferred multipolar atom model. In the crystal, symmetrical pairs of strong N-H⋯O hydrogen bonds connect the mol-ecules into dimers with an R 2 2 (8) ring motif. The inter-actions between neighbouring dimers are mostly van der Waals, between hydro-phobic methyl groups. Hirshfeld surface analysis shows the major contributions to the crystal packing are from H⋯H (42.6%) and O⋯H (26.7%) contacts., (© El Mestehdi et al. 2022.)

Possible polymorphic forms of the chemotherapy drug, temozolomide were predicted from the ab initio and DFT methods. The lattice minimization via distributed multipole analysis was carried out for the hypothetical generated structures. A crystal with unit cell parameters close to the real one and of same space group was retrieved, with partly similar packing and interactions. The analysis of inter molecular interaction (through Hirshfeld surface) and electrostatic potential reveals the complementary sites in the molecule. The 26 predicted structures were analyzed with respect to two computed lattice energies and hydrogen-bond propensity. The lattice energy of the real crystal [EXP] packing ranked number 6 compared on the basis of DMACRYS software and number 3 on the basis of the total lattice energy issued from the Crystalexplorer17 software at the B3LYP/6-31G∗∗ level of theory. The molecule has two strong hydrogen bond donors and five strong acceptors. The predicted packings are stabilized by one or two strong N-H…O/N-H…N as well as weak C-H…O/C-H…N and H…π hydrogen bonds. While the real structure with Z' = 1, EXP, forms only one strong H-bond (N-H…O=C), several of the predicted packings form two strong H-bonds. Two predicted crystal packings have unit cell parameters close to the real structure, one of them shares several common intermolecular interactions., Competing Interests: The authors declare no conflict of interest., (© 2022 The Author(s).)

A 3 × 3 isomer grid of nine N -(chlorophenyl)pyridinecarboxamides ( NxxCl ) is reported with physicochemical studies and single crystal structures ( Nx = pyridinoyl moiety; xCl = aminochlorobenzene ring; x = para -/ meta -/ ortho -), as synthesized by the reaction of the substituted p -/ m -/ o -pyridinecarbonyl chlorides ( Nx ) with p -/ m -/ o -aminochlorobenzenes ( xCl ). Several of the nine NxxCl crystal structures display structural similarities with their halogenated NxxX and methylated NxxM relatives ( x = p -/ m- / o -substitutions; X = F, Br; M = methyl). Indeed, five of the nine NxxCl crystal structures are isomorphous with their NxxBr analogues as the NpmCl / Br , NpoCl / Br , NmoCl / NmoBr , NopCl / Br , and NooCl / Br pairs. In the NxxCl series, the favored hydrogen bonding mode is aggregation by N-H···N pyridine interactions, though amide···amide intermolecular interactions are noted in NpoCl and NmoCl . For the NoxCl triad, intramolecular N-H···N pyridine interactions influence molecular planarity, whereas NppCl·H 2 O (as a monohydrate) exhibits O-H···O, N-H···O1W, and O1W-H···N interactions as the primary hydrogen bonding. Analysis of chlorine-containing compounds on the CSD is noted for comparisons. The interaction environments are probed using Hirshfeld surface analysis and contact enrichment studies. The melting temperatures ( T m ) depend on both the lattice energy and molecular symmetry (Carnelley's rule), and the melting points can be well predicted from a linear regression of the two variables. The relationships of the T m values with the total energy, the electrostatic component, and the strongest hydrogen bond components have been analyzed., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

A new cocrystal hydrate of gallic acid with pyrazine (4GA, Py, 4H 2 O; GA 4 PyW 4 ) was obtained and characterized by single crystal X-ray diffraction. In addition to structure determination, experimental charge density analysis was carried out in terms of Multipole Modelling (MP), X-ray wavefunction refinement (XWR) and maximum entropy method (MEM). As a part of XWR, the structural refinement via Hirshfeld atom refinement was carried out and resulted in O-H bond lengths close to values from neutron diffraction. A systematic comparison of molecular conformations and aromatic interactions in this new cocrystal hydrate was performed with other existing polymorphs of gallic acid. In GA 4 PyW 4 , the two symmetry-independent gallic acid molecules have a syn COOH orientation and form the common (COOH) 2 dimeric synthon. The carboxyl C atom displays the characteristics of π-holes with electropositive regions above and below the molecular plane and engages in acceptor-donor interactions with oxygen atoms of acidic O-H groups and phenol groups of neighbouring gallic acid molecules. The signature of the π-hole was identified from experimental charge density analysis, both in static density maps in MP and XWR as well as dynamic density in MEM, but it cannot be pinned down to a specific atom-atom interaction. This study presents the first comparison between an XWR and a MEM experimental electron-density determination., (open access.)

Two novel complexes, [(C 7 H 10 NO 2 )CdCl 3 ] n (I) and [(C 7 H 9 NO 2 )CuCl 2 ],havebeen synthesized and characterized. Single crystal X-ray diffraction revealed that in compound (I), 2,6-dimethanol pyridinium acts as a monodentate ligand through the O atom of the hydroxyl group. Contrarily, the 2,6-dimethanol pyridine ligand interacts tridentately with the Cu(II) ion via the nitrogen atoms and the two oxygen (O, O') atoms of the two hydroxyl groups. The structure's intermolecular interactions were studied using contact enrichment ratios and Hirshfeld surfaces. Following metal coordination, numerous hydrogen connections between entities and parallel displacement stacking interactions between pyridine rings dictate the crystal packing of both compounds. The aromatic cycles generate layers in the crystal for both substances. Powder XRD measurements confirmed the crystalline sample phase purity. SEM confirmed the surface homogeneity, whereas EDX semi-quantitative analysis corroborated the composition. IR spectroscopy identified vibrational absorption bands, while optical UV-visible absorption spectroscopy investigated optical properties. The thermal stability of the two materials was tested using TG-DTA.

Cytochrome P450 2C9 (CYP2C9) is a major drug-metabolizing enzyme that represents 20% of the hepatic CYPs and is responsible for the metabolism of 15% of drugs. A general concern in drug discovery is to avoid the inhibition of CYP leading to toxic drug accumulation and adverse drug-drug interactions. However, the prediction of CYP inhibition remains challenging due to its complexity. We developed an original machine learning approach for the prediction of drug-like molecules inhibiting CYP2C9. We created new predictive models by integrating CYP2C9 protein structure and dynamics knowledge, an original selection of physicochemical properties of CYP2C9 inhibitors, and machine learning modeling. We tested the machine learning models on publicly available data and demonstrated that our models successfully predicted CYP2C9 inhibitors with an accuracy, sensitivity and specificity of approximately 80%. We experimentally validated the developed approach and provided the first identification of the drugs vatalanib, piriqualone, ticagrelor and cloperidone as strong inhibitors of CYP2C9 with IC values <18 μM and sertindole, asapiprant, duvelisib and dasatinib as moderate inhibitors with IC50 values between 40 and 85 μM. Vatalanib was identified as the strongest inhibitor with an IC50 value of 0.067 μM. Metabolism assays allowed the characterization of specific metabolites of abemaciclib, cloperidone, vatalanib and tarafenacin produced by CYP2C9. The obtained results demonstrate that such a strategy could improve the prediction of drug-drug interactions in clinical practice and could be utilized to prioritize drug candidates in drug discovery pipelines., Competing Interests: The authors have declared that no competing interests exist.

The mutual penetration of electron densities between two interacting molecules complicates the computation of an accurate electrostatic interaction energy based on a pseudo-atom representation of electron densities. The numerical exact potential and multipole moment (nEP/MM) method is time-consuming since it performs a 3D integration to obtain the electrostatic energy at short interaction distances. Nguyen et al. [(2018), Acta Cryst. A74, 524-536] recently reported a fully analytical computation of the electrostatic interaction energy (aEP/MM). This method performs much faster than nEP/MM (up to two orders of magnitude) and remains highly accurate. A new program library, Charger, contains an implementation of the aEP/MM method. Charger has been incorporated into the MoProViewer software. Benchmark tests on a series of small molecules containing only C, H, N and O atoms show the efficiency of Charger in terms of execution time and accuracy. Charger is also powerful in a study of electrostatic symbiosis between a protein and a ligand. It determines reliable protein-ligand interaction energies even when both contain S atoms. It easily estimates the individual contribution of every residue to the total protein-ligand electrostatic binding energy. Glutathione transferase (GST) in complex with a benzophenone ligand was studied due to the availability of both structural and thermodynamic data. The resulting analysis highlights not only the residues that stabilize the ligand but also those that hinder ligand binding from an electrostatic point of view. This offers new perspectives in the search for mutations to improve the interaction between the two partners. A proposed mutation would improve ligand binding to GST by removing an electrostatic obstacle, rather than by the traditional increase in the number of favourable contacts.

The variation of charge density of two-electron multicentre bonding (pancake bonding) between semi-quinone radicals with pressure and temperature was studied on a salt of 5,6-di-chloro-2,3-di-cyano-semi-quinone radical anion (DDQ) with 4-cyano- N -methyl-pyridinium cation (4-CN) using the Transferable Aspheric Atom Model (TAAM) refinement. The pancake-bonded radical dimers are stacked by non-bonding π-interactions. With rising pressure, the covalent character of interactions between radicals increases, and above 2.55 GPa, the electron density indicates multicentric covalent interactions throughout the stack. The experimental charge densities were verified and corroborated by periodic DFT computations. The TAAM approach has been tested and validated for atomic resolution data measured at ambient pressure; this work shows this approach can also be applied to diffraction data obtained at pressures up to several gigapascals., (© Milašinović et al. 2021.)

The present paper reports a theoretical investigation based on first-principles density functional theory calculations to predict the external morphology of the tetragonal GdVO 4 crystal from its internal structure. The Bravais-Friedel-Donnay-Harker (BFDH) method, attachment energy (AE) method and surface energy (SE) method were used in this study. Slice energies (cohesive, attachment and specific surface) of the three main crystal faces having (110), (101) and (200) orientation and their d hkl thicknesses were computed using CRYSTAL17 code, in the frame of a 2D periodic slab model. The relative growth rate (R hkl ) and the morphological importance (MI hkl ) for each unrelaxed and relaxed (hkl) face of interest were determined. Consequently, the crystal shapes predicted based upon BFDH, AE and SE methods were represented by the Wulff construction. The results of the morphology crystal predictions, based on the above methods, were compared both against each other and against the experimentally observed morphologies. A quite satisfactory agreement between the predicted and observed crystal morphologies is noticed.

The structure of the new salt 1-(o-tolyl)biguanidium chloride, C 9 H 14 N 5 + , has been determined by single-crystal X-ray diffraction. The salt crystallizes in the monoclinic space group C2/c. In this structure, the chloride and biguanidium hydrophilic ions are mostly connected to each other via N-H...N and N-H...Cl hydrogen bonds to form layers parallel to the ab plane around y = 1/3 and y = 2/3. The 2-methylbenzyl groups form layers between these layers around y = 0 and y = 1/2, with the methyl group forming C-H...π interactions with the aromatic ring. Intermolecular interactions on the Hirshfeld surface were investigated in terms of contact enrichment and electrostatic energy, and confirm the role of strong hydrogen bonds along with hydrophobic interactions. A correlation between electrostatic energy and contact enrichment is found only for the strongly attractive (N-H...Cl - , has been determined by single-crystal X-ray diffraction. The salt crystallizes in the monoclinic space group C2/c. In this structure, the chloride and biguanidium hydrophilic ions are mostly connected to each other via N-H...N and N-H...Cl hydrogen bonds to form layers parallel to the ab plane around y = 1/3 and y = 2/3. The 2-methylbenzyl groups form layers between these layers around y = 0 and y = 1/2, with the methyl group forming C-H...π interactions with the aromatic ring. Intermolecular interactions on the Hirshfeld surface were investigated in terms of contact enrichment and electrostatic energy, and confirm the role of strong hydrogen bonds along with hydrophobic interactions. A correlation between electrostatic energy and contact enrichment is found only for the strongly attractive (N-H...Cl - ) and repulsive contacts. Electrostatic energies between ions reveal that the interacting biguanidium cation pairs are repulsive and that the crystal is maintained by attractive cation...Cl - dimers. The vibrational absorption bands were identified by IR spectroscopy.

Polarizability is a key molecular property involved in either macroscopic (i.e., dielectric constant) and microscopic properties (i.e., interaction energies). In rigid molecules, this property only depends on the ability of the electron density (ED) to acquire electrostatic moments in response to applied electric fields. Databases of transferable electron density fragments are a cheap and efficient way to access molecular EDs. This approach is rooted in the relative conservation of the atomic ED between different molecules, termed transferability principle. The present work discusses the application of this transferability principle to the polarizability, an electron density-derived property, partitioned in atomic contributions using the Quantum Theory of Atoms In Molecules topology. The energetic consequences of accounting for in situ deformation (polarization) of database multipolar atoms are investigated in detail by using a high-quality quantum chemical benchmark.

The title compound, [Ni(C 10 H 8 N 2 ) 3 ](C 9 H 5 N 4 O) 2 ·2H 2 O, crystallizes as a racemic mixture in the monoclinic space group C 2/ c . In the crystal, the 1,1,3,3-tetracyano-2-ethoxypropenide anions and the water molecules are linked by O-H⋯N hydrogen bonds, forming chains running along the [010] direction. The bpy ligands of the cation are linked to the chain via C-H⋯π(cation) inter-actions involving the CH 3 group. The inter-molecular inter-actions were investigated by Hirshfeld surface analysis and two-dimensional fingerprint plots.

Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance-covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Å resolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling., (open access.)

A comparative study of syn vs anti carboxylic acids in hybrid peptides based on experimental electron density studies and theoretical calculations shows that, in the anti form, all three bond angles surrounding C carboxyl of the -COOH group are close to ∼120°, as expected for a C-sp 2 atom, whereas in the syn form, the ∠C α -C(O)-O hydroxyl angle is significantly smaller by 5-10°. The oxygen atom in the carboxyl group is more electronegative in the anti form, so the polarity of the acidic O-H bond is higher in the anti form compared to the syn form, as observed within the limitations of H atom treatment in X-ray diffraction. Consequently, the investigated anti carboxylic acid forms the strongest O-H···O hydrogen bond among all model compounds. Furthermore, according to natural bond orbital analysis, the oxygen lone pairs are clearly nonequivalent, as opposed to the general notion of hybridization of equivalent sp 2 and sp 3 lone pairs on carbonyl or hydroxyl oxygen atoms. The hybridization of the lone pairs is directly related to the directionality and strength of hydrogen bonds.

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

The electron density distribution of [PPh 4 ][UF 6 ] was obtained from high-resolution X-ray diffraction data measured at 20 K. The electron density was modeled with an augmented Hansen-Coppens multipolar formalism. Topological analysis reveals that the U-F bond is of incipient covalent nature. Theoretical calculations add further support to the bonding description gleaned from the experimental model. The impact of the uranium anomalous dispersion terms on the refinement is also discussed.

The crystal contacts of several families of hydrocarbon compounds substituted with one or several types of oxygenated chemical groups were analyzed statistically using the Hirshfeld surface methodology. The propensity of contacts to occur between two chemical types is described with the contact enrichment descriptor. The systematic large enrichment ratios of some interactions like the O-H⋯O hydrogen bonds suggests that these contacts are a driving force in the crystal packing formation. The same statement holds for the weaker C-H⋯O hydrogen bonds in ethers, esters and ketones, in the absence of polar H atoms. The over-represented contacts in crystals of oxygenated hydrocarbons are generally of two types: electrostatic attractions (hydrogen bonds) and hydrophobic interactions. While Cl⋯O interactions are generally avoided, in a minority of chloro-oxygenated hydrocarbons, significant halogen bonding does occur. General tendencies can often be derived for many contact types, but outlier compounds are instructive as they display peculiar or rare features. The methodology also allows the detection of outliers which can be structures with errors. For instance, a significant number of hydroxylated molecules displaying over-represented non-favorable oxygen-oxygen contacts turned out to have wrongly oriented hydroxyl groups. Beyond crystal packings with a single molecule in the asymmetric unit, the behavior of water in monohydrate compounds and of crystals with Z ' = 2 (dimers) are also investigated. It was found in several cases that, in the presence of several oxygenated chemical groups, cross-interactions between different chemical groups ( e.g. water/alcohols; alcohols/phenols) are often favored in the crystal packings. While some trends in accordance with common chemical principles are retrieved, some unexpected results can however appear. For example, in crystals of alcohol-phenol compounds, the strong O-H⋯O hydrogen bonds between two phenol groups turn out to be extremely rare, while cross contacts between phenols and alcohols have enriched occurrences.

Neuropilin-1 (NRP-1), a transmembrane glycoprotein acting as a co-receptor of VEGF-A, is expressed by cancer and angiogenic endothelial cells and is involved in the angiogenesis process. Taking advantage of functionalities and stereodiversities of sugar derivatives, the design and the synthesis of carbohydrate based peptidomimetics are here described. One of these compounds (56) demonstrated inhibition of VEGF-A 165 binding to NRP-1 (IC 50 =39μM) and specificity for NRP-1 over VEGF-R2. Biological evaluations were performed on human umbilical vein endothelial cells (HUVECs) through activation of downstream proteins (AKT and ERK phosphorylation), viability/proliferation assays and in vitro measurements of anti-angiogenic abilities., (Copyright © 2016. Published by Elsevier Ltd.)

Betulin derivatives are a widely studied group of compounds of natural origin due to their wide spectrum of biological activities. This paper describes new betulin derivatives, containing a phosphonate group. The allyl-vinyl isomerization and synthesis of acetylenic derivatives have been reported. Structural identification of products as E and Z isomers has been carried out using ¹H-, (13)C-, (31)P-NMR, and crystallographic analysis. The crystal structure in the orthorhombic space group and analysis of crystal packing contacts for 29-diethoxyphosphoryl-28-cyclopropylpropynoyloxy-lup-20E(29)-en-3β-ol 8a are reported. All new compounds were tested in vitro for their antiproliferative activity against human T47D (breast cancer), SNB-19 (glioblastoma), and C32 (melanoma) cell lines.

Due to both technical and methodological difficulties, determining and analyzing charge densities of very large molecular systems represents a serious challenge that, in the crystallographers community, has been mainly tackled by observing that the so-called pseudoatoms of the electron density multipole expansions are reliably transferable from molecule to molecule. This has led to the construction of pseudoatoms databanks that have allowed successful refinements of crystallographic structures of macromolecules, while taking into account their corresponding reconstructed electron distributions. A recent alternative/complement to the previous approach is represented by techniques based on extremely localized molecular orbitals (ELMOs) that, due to their strict localization on small molecular fragments (e.g., atoms, bonds, and functional groups), are also in principle exportable from system to system. The ELMOs transferability has been already tested in detail, and, in this work, it has been compared to the one of the pseudoatoms. To accomplish this task, electron distributions obtained both through the transfer of pseudoatoms and through the transfer of extremely localized molecular orbitals have been analyzed, especially taking into account topological properties and similarity indexes. The obtained results indicate that all the considered reconstruction methods give completely reasonable and similar charge densities, and, consequently, the new ELMOs libraries will probably represent new useful tools not only for refining crystal structures but also for computing approximate electronic properties of very large molecules.

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

The likelihood of occurrence of intermolecular contacts in crystals of halogenated organic compounds has been analysed statistically using tools based on the Hirshfeld surface. Several families of small halogenated molecules (containing organic F, Cl, Br or I atoms) were analysed, based on chemical composition and aromatic or aliphatic character. The behaviour of crystal contacts was also probed for molecules containing O or N. So-called halogen bonding (a halogen making short interactions with O or N, or a π interaction with C) is generally disfavoured, except when H is scarce on the molecular surface. Similarly, halogen⋯halogen contacts are more rare than expected, except for molecules that are poor in H. In general, the H atom is found to be the preferred partner of organic halogen atoms in crystal structures. On the other hand, C⋯C interactions in parallel π-stacking have a high propensity to occur in halogenated aromatic molecules. The behaviour of the four different halogen species (F, Cl, Br, I) is compared in several chemical composition contexts. The analysis tool can be refined by distinguishing several types for a given chemical species, such as H atoms bound to O or C. Such distinction shows, for instance, that C-H⋯Cl and O-H⋯O are the preferred interactions in compounds containing both O and Cl.

Examination of protein structure at the subatomic level is required to improve the understanding of enzymatic function. For this purpose, X-ray diffraction data have been collected at 100 K from cholesterol oxidase crystals using synchrotron radiation to an optical resolution of 0.94 Å. After refinement using the spherical atom model, nonmodelled bonding peaks were detected in the Fourier residual electron density on some of the individual bonds. Well defined bond density was observed in the peptide plane after averaging maps on the residues with the lowest thermal motion. The multipolar electron density of the protein-cofactor complex was modelled by transfer of the ELMAM2 charge-density database, and the topology of the intermolecular interactions between the protein and the flavin adenine dinucleotide (FAD) cofactor was subsequently investigated. Taking advantage of the high resolution of the structure, the stereochemistry of main-chain bond lengths and of C=O···H-N hydrogen bonds was analyzed with respect to the different secondary-structure elements.

The title salt, C3H6N3S2 (+)·Cl(-)·H2O, crystallized with two organic cations, two chloride anions and two water mol-ecules in the asymmetric unit. The methyl C atoms deviate from their respective bound ring planes by 0.081 and 0.002 Å. In the crystal, the components are connected via N-H⋯O, N-H⋯Cl and O-H⋯Cl hydrogen bonds, forming sheets lying parallel to (100). The sheets are linked into bilayers by O-H⋯Cl hydrogen bonds involving the chloride ions and water mol-ecules. Within the bilayers there are π-π inter-actions [inter-centroid distances = 3.4654 (4) and 3.4789 (4) Å] involving inversion-related cations.

In the title hydrated mol-ecular salt, 2C5H8N3O(+)·SO4 (2-)·H2O, the components are linked by N-H⋯Os and Ow-H⋯Os (s = sulphate, w = water) hydrogen bonds, generating a layer by a+b+c and 2a-b translations. The cations are arranged nearly in parallel and show displaced π-π stacking centroid-centroid distance = 4.661 (2) Å between adjacent layers.

The asymmetric unit of the title compound, [K3(C4H2N3O4)3(H2O)2] n , contains two potassium cations (one in general position, one located on a twofold rotation axis), one and a half oxonate anions (the other half generated by twofold symmetry) and one water mol-ecule. As a result of the twofold symmetry, one H atom of the symmetric anion is statistically occupied. Both potassium cations are surrounded by eight oxygen atoms in the form of distorted polyhedra. Adjacent cations are inter-connected by oxygen bridges, generating layers parallel to (100). The aromatic ring system of the oxonate anions link these layers into a network structure. The crystal packing is stabilized by N-H⋯O, O-H⋯O and O-H⋯N hydrogen bonds, three of which are bifurcated. In addition, inter-molecular π-π stacking inter-actions exist between neighboring aromatic rings with a centroid-centroid distance of 3.241 (2) Å.

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Å resolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen-Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O-H···O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C-C=C-OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

The partitioning of space with Hirshfeld surfaces enables the analysis of fingerprint molecular interactions in crystalline environments. This study uses the decomposition of the crystal contact surface between pairs of interacting chemical species to derive an enrichment ratio. This quantity enables the analysis of the propensity of chemical species to form intermolecular interactions with themselves and other species. The enrichment ratio is obtained by comparing the actual contacts in the crystal with those computed as if all types of contacts had the same probability to form. The enrichments and contact tendencies were analyzed in several families of compounds, based on chemical composition and aromatic character. As expected, the polar contacts of the type H⋯N, H⋯O and H⋯S, which are generally hydrogen bonds, show enrichment values larger than unity. O⋯O and N⋯N contacts are impoverished while H⋯H interactions display enrichment ratios which are generally close to unity or slightly lower. In aromatic compounds, C⋯C contacts can display large enrichment ratios due to extensive π⋯π stacking in the crystal packings of heterocyclic compounds. C⋯C contacts are, however, less enriched in pure (C,H) hydrocarbons as π⋯π stacking is not so favourable from the electrostatic point of view compared with heterocycles. C⋯H contacts are favoured in (C,H) aromatics, but these interactions occur less in compounds containing O, N or S as some H atoms are then involved in hydrogen bonds. The study also highlights the fact that hydrogen is a prefered interaction partner for fluorine.

Bromoethyl sulfonium trifluoromethanesulfonate is a salt complex in which a sulfur atom makes three covalent bonds. This molecule has been proved to act as an efficient annulation reagent which results in formation of synthetically challenging and pharmaceutically important 4-, 5-, 6-, and 7-membered heterocycles in excellent yields. The charge density of the molecule was determined from both experimentally and theoretically derived diffraction data. The stereochemistry and electron density topology of the sulfonium group was analyzed. To understand the chemical reactivity of the molecule, the electrostatic potential difference between the two carbon atoms of the bromoethyl group was investigated. It has been considered that the hydrogen atoms on the carbon atom bound to sulfur are more acidic in character due to their vicinity with the triply covalently bonded positively charged sulfur atom. The electropositivity of the S-attached and Br-attached methylene groups are compared in the experimental and theoretical charge densities using topological atomic charges and electrostatic potential at the molecular surface.

In the crystal structure of the title organic-inorganic hybrid material, (C10H22N2)[ZnCl4], the tetrachloridozincate anions and 1-cyclohexylpiperazine-1,4-diium dications are interconnected via N-H...Cl and C-H...Cl hydrogen bonds to form layers parallel to the (001) plane. The cyclohexyl groups from adjacent chains interdigitate, thus building the three-dimensional structure. The piperazinium and cyclohexyl rings exhibit regular spatial chair conformations. The title salt was also characterized by FT-IR and Raman spectroscopic analyses.

Background: Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms., Results: A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed., Conclusions: A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.

In the title mol-ecular salt, C6H10N2 (2+)·NO3 (-)·Cl(-), the complete cation is generated by a crystallographic mirror plane. The complete nitrate ion is also generated by reflection, with the N atom and one O atom lying on the mirror plane; the chloride ion also lies on the reflection plane. In the crystal, the components are linked by N-H⋯Cl and N-H⋯(N,O) hydrogen bonds, forming (001) layers with the benzene rings projecting into the inter-layer regions. The layers are linked by weak C-H⋯O hydrogen bonds, generating a three-dimensional network.

The electron-density distribution of a new crystal form of coumarin-102, a laser dye, has been investigated using the Hansen-Coppens multipolar atom model. The charge density was refined versus high-resolution X-ray diffraction data collected at 100 K and was also constructed by transferring the charge density from the Experimental Library of Multipolar Atom Model (ELMAM2). The topology of the refined charge density has been analysed within the Bader `Atoms In Molecules' theory framework. Deformation electron-density peak heights and topological features indicate that the chromen-2-one ring system has a delocalized π-electron cloud in resonance with the N (amino) atom. The molecular electrostatic potential was estimated from both experimental and transferred multipolar models; it reveals an asymmetric character of the charge distribution across the molecule. This polarization effect is due to a substantial charge delocalization within the molecule. The molecular dipole moments derived from the experimental and transferred multipolar models are also compared with the liquid and gas-phase dipole moments. The substantial molecular dipole moment enhancements observed in the crystal environment originate from the crystal field and from intermolecular charge transfer induced and controlled by C-H···O and C-H···N intermolecular hydrogen bonds. The atomic forces were integrated over the atomic basins and compared for the two electron-density models.

Three models of charge-density distribution - Hansen-Coppens multipolar, virtual atom and kappa - of different complexities, different numbers of refined parameters, and with variable levels of restraints, were tested against theoretical and high-resolution X-ray diffraction structure factors for 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitrile. The influence of the model, refinement strategy, multipole level and treatment of the H atoms on the dipole moment was investigated. The dipole moment turned out to be very sensitive to the refinement strategy. Also, small changes in H-atom treatment can greatly influence the calculated magnitude and orientation of the dipole moment. The best results were obtained when H atoms were kept in positions determined by neutron diffraction and anisotropic displacement parameters (obtained by SHADE, in this case) were used. Also, constraints on kappa values of H atoms were found to be superior to the free refinement of these parameters. It is also shown that the over-parametrization of the multipolar model, although possibly leading to better residuals, in general gives worse dipole moments.

ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations., (© 2012 International Union of Crystallography)

The projector augmented wave (PAW) methodology has been used to calculate a high precision electron density distribution ρ(r) for the hexachlorobenzene crystal phase. Implementing the calculation of the crystallographic structure factors in the VASP code has permitted one to obtain the theoretical multipolar ρ(r). This electron density is compared with both the DFT electron density and the experimental multipolar model obtained from high-resolution X-ray diffraction data. This comparison has been carried out in intra- and intermolecular regions within the framework of the quantum theory of atoms-in-molecules (QTAIM) developed by Bader and co-workers. The characterization of the electron density in both C-Cl and Cl···Cl regions, as well as within the atomic basins, shows similar features for the three models. As a consequence, the observation of charge depletion and charge concentration regions around the halogen nuclei (along the C-Cl bonding axis and in the perpendicular plane, respectively) underlines the nature of halogen bonding in terms of electrophilic and nucleophilic interactions.

The experimental charge density distribution was determined for 2-methyl-4-nitro-1-phenyl-1H-imidazole-5-carbonitryle, using the Hansen-Coppens multipole model. Free R factor calculations were performed with MoPro software to find optimal restraints for a physically meaningful model. The crystal packing is determined to some extent by weak C-H···O and C-H···N hydrogen bonds but mostly by a lateral electrostatic interaction between antiparallel side-by-side C≡N groups. Electrostatic energy calculations were performed based on the experimental data and are in line with the high-level, explicitly correlated theoretical SCS-RI-MP2-F12 calculations of total energy. The molecular dipole moment and atomic charge values were compared for different experimental and theoretical models, to highlight the dependence of the electrostatic property outputs on the applied restraints. Interesting O···O contacts are also described. The results are compared with two recently investigated nitroimidazole derivatives, namely, 1-(2'-aminophenyl)-2-methyl-4-nitroimidazole and 1-phenyl-4-nitroimidazole.

Helices represent the most abundant secondary structure motif in proteins and are often involved in various functional roles. They are stabilized by a network of hydrogen bonds between main chain carbonyl and amide groups. Several surveys scrutinized these hydrogen bonds, mostly based on the geometry of the interaction. Alternatively, the topological analysis of the electron density provides a powerful technique to investigate hydrogen bonds. For the first time, transferred experimental charge density parameters (ELMAM database) were used to carry out a topological analysis of the electron density in protein helices. New parameters for the description of the hydrogen bond geometry are proposed. Bonding contacts between the amide N and carbonyl O atoms (N···O) of helices, poorly addressed in the literature so far, were characterized from topological, geometrical, and local energetic analyses. Particularly, a geometrical criterion allowing for the discrimination between hydrogen bonds and N···O contacts is proposed.

The title compound, C(16)H(16)Br(2)O(4)S(2), which is a precursor for the synthesis of oligothiophenes and their substituted homologues, was synthesized and its X-ray crystal structure determined at 100 K. The experimental electron-density parameters for the available atom types were transferred from the ELMAM2 database. The compound lies about an inversion centre, which coincides with the mid-point of a C-C bond. The molecules in the crystal are linked by several types of weak interactions; the largest contact surfaces are for H...H and H...Br.

The experimental charge-density distribution was determined for 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole crystals. An anharmonic model was applied to the N atoms of both amino groups and to one nitro group in order to account for high residual peaks after harmonic multipole refinement and to obtain a better charge-density model. Free R-factor calculations [Brünger (1992). Nature, 355, 472-475] with restrained models implemented in MoPro were used to determine the degree of similarity of the two symmetry-independent molecules in the unit cell. The results are compared with 1-phenyl-4-nitroimidazole in order to analyze the influence of the amine and methyl functional groups. The asymmetric unit contains two symmetry-independent molecules giving rise to a dimer connected via strong N-H···N hydrogen bonds; these dimers are the building blocks of the crystal. In the crystal structure there are also weaker interactions and many short directional contacts (C-H···O, C-H···N and C-H···π), for which the Koch-Popelier topological criteria were applied. This analysis revealed that the C-H···π interactions lie at the border between weak hydrogen bonds and van der Waals interactions. Special attention was also paid to stabilizing H···H interactions. It turned out that the electron density, Laplacian and density energies at the critical points show an exponential dependence on the contact distance, similar to the relation found for other interactions.

The experimental distribution of electron density in Ph(3)(4,5-OMe-3,6-Bu(t)-Cat)Sb·MeCN (1*) and Ph(3)(4,5-N(2)C(4)H(6)-3,6-Bu(t)-Cat)Sb·MeOH (2*) complexes was studied. According to atoms in molecules theory, the Sb-C(Ph), Sb-O(catecholate), and Sb···N(O) bonds are intermediate, whereas the O-C and C-C bonds are covalent, respectively. The energy of the Sb···N(MeCN) and Sb···O(MeOH) bonds are 7.0 and 11.3 kcal/mol according to the Espinosa equation. Density functional theory and Hartree-Fock calculations were carried out for a series of catecholate and amidophenolate complexes of antimony(V). It was shown that such calculations reliably reproduce geometrical and topological parameters and therefore can be used for a criterion search of dioxygen reversible binding by the catecholate and amidophenolate complexes of antimony(V). It was found that the "critical" value of the HOMO energy vary in the range from -5.197 to -5.061 eV for reversible binding of dioxygen complexes. This can serve as a thermodynamic criterion to predict the possibility of the dioxygen reversible binding by the catecholate and amidophenolate complexes of Sb(V). The HOMO energies correlate with the conversion of the catecholate and amidophenolate complexes in corresponding spiroendoperoxide derivatives as well. The contribution of the atom orbitals of the carbon atoms in the five-membered metallocycle to HOMO in complexes with different substitutes in the 4- and 5-positions of the catecholate ligand allows predicting the place of dioxygen addition., (© 2011 American Chemical Society)

Nitramines and related N-nitro compounds have attracted significant attention owing to their use in rocket fuel and as explosives. The charge density of 1-nitroindoline was determined experimentally and from theoretical calculations. Electron-density refinements were performed using the multipolar atom formalism. In order to design the ideal restraint strategy for the charge-density parameters, R-free analyses were performed involving a series of comprehensive refinements. Different weights were applied to the charge-density restraints, namely the similarity between chemically equivalent atoms and local symmetry. Additionally, isotropic thermal motion and an anisotropic model calculated by rigid-body analysis were tested on H atoms. The restraint weights which resulted in the lowest values of the averaged R-free factors and the anisotropic H-atom model were considered to yield the best charge density and were used in the final refinement. The derived experimental charge density along with intra- and intermolecular interactions was analysed and compared with theoretical calculations, notably with respect to the symmetry of multipole parameters. A comparison of different refinements suggests that the appropriate weighting scheme applied to charge-density restraints can reduce the observed artefacts. The topological bond orders of the molecule were calculated.

The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high-resolution single-crystal X-ray diffraction experiment on L-His-L-Ala dihydrate and 23 K high-resolution data for L-Ala [Destro & Marsh (1988). J. Phys. Chem. 92, 966-973], the structural properties, electron-density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal-field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly-L-His dihydrate, D,L-His and the above-mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root-mean-square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X-H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high-resolution and low-resolution data, respectively. Differences in dipole-moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9-15 and 22-33 kJ mol(-1) for UBDB and the other database models, respectively.