Experimental Electrostatic Potential Research Articles

TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules.

3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.

Reduced Occupancy of the Oxygen-Evolving Complex of Photosystem II Detected in Cryo-Electron Microscopy Maps.

Computational simulations of electrostatic potentials (ESPs), based on atomistic models and independent atomic scattering factors, have remained challenging when applied to the oxygen-evolving complex (OEC) of photosystem II (PSII). Here, we overcome that challenge by using an ESP function obtained with density functional theory and atomic coordinates for the OEC of PSII obtained by optimization of the dark-adapted S1 state. We find that the ESP is much higher for the OEC than for the nearby reference side chain of amino acid residue D1-H190. In contrast, experimental ESP maps recently published for two PSII-light-harvesting complex II super-complexes show that the ESP of the OEC is approximately half the value of the D1-H190 side chain. The apparent disparity is attributed to a reduced 31-38% occupancy of the OEC, likely associated with its reduction by electron scattering.

Identification of ions in experimental electrostatic potential maps.

Cryo-electron microscopy (cryo-EM) directly images the distribution of electrostatic potential (ESP) within macromolecules, and thus can provide much more information about atomic charge than X-ray crystallography. The electron-scattering length of an isolated ion is quite different from that of the corresponding neutral atom. The difference is very large at small scattering angles where the effects of electron distributions are largest, but becomes smaller at high scattering angles where nuclear charge determines outcomes. For this reason, in cryo-EM maps that have been solved at resolutions lower than ∼2.5 Å, peaks corresponding to anions will always be less prominent than those of cations, and may even be negative. Furthermore, if a map of this kind is smeared computationally after the fact, which reduces its effective resolution, anion peaks will diminish in size, cation peaks will grow and peaks that represent uncharged atoms will remain about the same. These effects can be used to determine the sign of the charges carried by the ions associated with a macromolecule and even estimate their magnitudes. The ESP value for a cation in a cation-anion pair is smaller than the value of the cation in isolation, but the ESP value for the anion in the ionic pair is greater than the value of the anion in isolation. The experimental range of ESP values for Mg2+ relative to that of the closest C1' atom is found to be between 0.57 and 1.27.

Effects of aligned α-helix peptide dipoles on experimental electrostatic potentials.

Aligned protein α-helix dipoles have been implicated in protein function and structure. The recent breakthroughs in high-resolution electron microscopy (EM) of macromolecules makes it possible to explore fundamental aspects of structural biology at the detailed molecular level. The electrostatic potential (ESP) generated by aligned protein α-helix dipole should be observable in high-resolution EM maps despite the fact that the effect may be partially screened by induced electric fields. Here, we show that aligned backbone dipoles in protein α-helices account for long-range features in the protein ESP functions. Our results are consistent with experimental EM maps and density functional theory calculations, including direct Fourier summation for proper calculation of the ESP due to the nonlocal nature of the ESP function from aligned dipoles and other partial atomic charges.

Experimental charge density from electron microscopic maps.

The charge density (CD) distribution of an atom is the difference per unit volume between the positive charge of its nucleus and the distribution of the negative charges carried by the electrons that are associated with it. The CDs of the atoms in macromolecules are responsible for their electrostatic potential (ESP) distributions, which can now be visualized using cryo-electron microscopy at high resolution. CD maps can be recovered from experimental ESP density maps using the negative Laplacian operation. CD maps are easier to interpret than ESP maps because they are less sensitive to long-range electrostatic effects. An ESP-to-CD conversion involves multiplication of amplitudes of structure factors as Fourier transforms of these maps in reciprocal space by 1/d2 , where d is the resolution of reflections. In principle, it should be possible to determine the charges carried by the individual atoms in macromolecules by comparing experimental CD maps with experimental ESP maps.

On contribution of known atomic partial charges of protein backbone in electrostatic potential density maps.

Partial charges of atoms in a molecule and electrostatic potential (ESP) density for that molecule are known to bear a strong correlation. In order to generate a set of point-field force field parameters for molecular dynamics, Kollman and coworkers have extracted atomic partial charges for each of all 20 amino acids using restrained partial charge-fitting procedures from theoretical ESP density obtained from condensed-state quantum mechanics. The magnitude of atomic partial charges for neutral peptide backbone they have obtained is similar to that of partial atomic charges for ionized carboxylate side chain atoms. In this study, the effect of these known atomic partial charges on ESP is examined using computer simulations and compared with the experimental ESP density recently obtained for proteins using electron microscopy. It is found that the observed ESP density maps are most consistent with the simulations that include atomic partial charges of protein backbone. Therefore, atomic partial charges are integral part of atomic properties in protein molecules and should be included in model refinement.

On the appearance of carboxylates in electrostatic potential maps.

Electron microscopy can provide accurate, high-resolution images of the distribution of electrostatic potential (ESP) in biological macromolecules. Careful examination of ESP maps that have been published for peptides and proteins at resolution ranging from 1.0 Å to 2.9 Å reveals that the negative charges of carboxylate groups have a profound effect on their appearance. It is clear that investigators must take the negative features in their experimental ESP maps into account when modeling the conformations of Asp and Glu side chains and those of the residues that surround them.

Theoretical and experimental electrostatic potential around the m-nitrophenol molecule.

This work concerns a comparison of experimental and theoretical results of the electron charge density distribution and the electrostatic potential around the m-nitrophenol molecule (m-NPH) known for its interesting physical characteristics. The molecular experimental results have been obtained from a high-resolution X-ray diffraction study. Theoretical investigations were performed using the Density Functional Theory at B3LYP level of theory at 6-31G* in the Gaussian program. The multipolar model of Hansen and Coppens was used for the experimental electron charge density distribution around the molecule, while we used the DFT methods for the theoretical calculations. The electron charge density obtained in both methods allowed us to find out different molecular properties such us the electrostatic potential and the dipole moment, which were finally subject to a comparison leading to a good match obtained between both methods. The intramolecular charge transfer has also been confirmed by an HOMO-LUMO analysis.

ChemInform Abstract: New Synthesis of trans-Disubstituted Cyclam Macrocycles - Elucidation of the Disubstitution Mechanism on the Basis of X-Ray Data and Molecular Modeling.

A new way to synthesize trans-disubstituted cyclam tetraazamacrocycles 1 is reported. The synthesis proceeds in three steps via the tricyclic 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane system 2, which can be selectively dialkylated and hydrolyzed under basic conditions to give the final product 1. An understanding of the reactivity, based on the X-ray experimental electrostatic potential and molecular modeling of the 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane macrotricycle, has permitted the elucidation of a new reaction pathway leading to the trans-disubstituted cyclam.

Charge-density studies of energetic materials: CL-20 and FOX-7

Experimental electron densities and derived properties have been determined for the two energetic materials CL-20 (3,5,9,11-tetraacetyl-14-oxo-1,3,5,7,9,11-hexaazapentacyclo-[5.5.3.02,6.04,10.08,12]pentadecane), and FOX-7 (1,1-diamino-2,2-dinitroethylene) from single-crystal diffraction. Synchrotron data extending to high scattering angles were measured at low temperature. Low figures-of-merit and excellent residuals were obtained. The Hansen & Coppens multipole-model electron density was compared with results from theoretical calculations via structure factors simulating an experiment. Chemical bonding in the molecules is discussed and a topological analysis gives insight especially into the character of those bonds that are thought to play a key role in the decomposition of the molecules. A comparison of theoretical and experimental electrostatic potentials shows no obvious evidence supporting earlier findings on other nitroheterocyclic molecules that electron-density maxima near the C-NO(2) bonds mapped on the electron-density isosurface can be correlated with impact sensitivities. For FOX-7 periodic Hartree-Fock calculations were performed to investigate the influence of the crystal field on the electron density distribution.

Experimental/Theoretical Electrostatic Properties of a Styrylquinoline-Type HIV-1 Integrase Inhibitor and Its Progenitors

We have established that polyhydroxylated styrylquinolines are potent inhibitors of HIV-1 integrase (IN). Among them, we have identified (E)-8-hydroxy-2-[2-(4,5-dihydroxy-3-methoxyphenyl)-ethenyl]-7-quinolinecarboxylic acid (1) as a promising lead. Previous molecular dynamics simulations and docking procedures have shown that the inhibitory activity involves one or two metal cations (Mg2+), which are present in the vicinity of the active center of the enzyme. However, such methods are generally based on a force-field approach and still remain not as reliable as ab initio calculations with extended basis sets on the whole system. To go further in this area, the aim of the present study was to evaluate the predictive ability of the electron density and electrostatic properties in the structure-activity relationships of this class of HIV-1 antiviral drugs. The electron properties of the two chemical progenitors of 1 were derived from both high-resolution X-ray diffraction experiments and ab initio calculations. The twinning phenomenon and solvent disorder were observed during the crystal structure determination of 1. Molecule 1 exhibits a planar s-trans conformation, and a zwitterionic form in the crystalline state is obtained. This geometry was used for ab initio calculations, which were performed to characterize the electronic properties of 1. The electron densities, electrostatic potentials, and atomic charges of 1 and its progenitors are here compared and analyzed. The experimental and theoretical deformation density bond peaks are very comparable for the two progenitors. However, the experimental electrostatic potential is strongly affected by the crystal field and cannot straightforwardly be used as a predictive index. The weak difference in the theoretical electron densities between 1 and its progenitors reveals that each component of 1 conserves its intrinsic properties, an assumption reinforced by a 13C NMR study. This is also shown through an excellent correlation of the atomic charges for the common fragments. The electrostatic potential minima in zwitterionic and nonzwitterionic forms of 1 are discussed in relation with the localization of possible metal chelation sites.

Elusive contribution of the experimental surface molecular electrostatic potential and promolecule approximation in the empirical estimate of the crystal density

The aim of this study is to probe the crystal density (D(c)) description in terms of pertinent molecular characteristics and properties. In this purpose, the electrostatic potential was derived from available experimental electron density multipole parameters of molecular compounds with different D(c) magnitudes. The surface electrostatic potential has been analyzed through the positive and negative statistical variances. The surface of the molecule is here corresponding to particular isodensity values according to Bader's topological theory. Following the successful Politzer's method based on quantum mechanics calculations to empirically describe macroscopic properties, the crystal density was regressed on the molecular density and the surface electrostatic potential variance. This latter appears to be a poor statistical descriptor of the crystal density when the experimentally derived electrostatic potential is used and it does not significantly improve the fit of D(c) to molecular density alone. Compared to Politzer's approach based on gas phase isolated molecules, the experimental electrostatic potential is biased by the interactions in the crystal lattice. As an alternative to other sophisticated methods, the promolecule isodensity surface offers a quite useful and straightforward way to define the molecular volumes. The reported description of the crystal density for a set of 50 molecules using the promolecule approach yields satisfactory results.

Charge density and experimental electrostatic potentials of two penicillin derivatives.

Two penicillin derivatives, the active penamecillin and the inactive penamecillin-1beta-sulfoxide, were used to study the relationship between their charge density and their activity. Single crystals of both compounds were measured at the synchrotron beamline F1 at the HASYLAB/DESY, at 100 K and up to resolutions of around 0.4 A. Experimental charge densities were obtained by using the Hansen-Coppens multipole formalism. The cleavage of the amide bond in the beta-lactam ring is of paramount importance in the mechanism of action of penicillins. Topological analysis of this bond in terms of Bader's AIM theory showed that its strength is equal in both compounds; therefore a direct influence of bond strength on the activity can be ruled out. However, the two derivatives differ significantly in their experimental electrostatic potentials. These differences are discussed and provide further insight into the chemistry and activity of penicillins.

Gradient vector field and properties of the experimental electrostatic potential: Application to ibuprofen drug molecule

The present study focuses on the electric field features and related physical properties which can be derived from the topology of the experimental electrostatic potential. These properties were retrieved from the electron density multipole refinement of high-resolution x-ray data collected on a racemic crystal of ibuprofen drug. The electric field lines are depicted around the molecule revealing gradient vector zero flux atomic basins and critical points (CP’s) having a different significance than that brought out by the topology of the electron density. This method emphasizes a partioning of the molecular system mainly governed by the nuclear–electron interaction. The concept of Slater’s nuclear screening is here explored from the inspection of the gradient field zero flux surface separating the atoms in the molecule. Moreover, empirical parameters like covalent or atomic bond radii are accurately estimated from CP–atom distances in the molecular heteroatomic bonds. The local minima of the electrostatic potential are searched around the ibuprofen molecule in order to locate the binding sites for further molecular interactions with biological targets or with excipients in pharmaceutical preparations. Ibuprofen dipole moment is also estimated by a method based upon the fit to the experimental electrostatic potential values generated around the molecule.

Experimental charge density and electrostatic potential of glycyl-L-threonine dihydrate.

The experimental electron density distribution in glycyl-L-threonine dihydrate has been investigated using single-crystal X-ray diffraction data at 110 K to a resolution of (sin theta/lambda) = 1.2 A(-1). Multipolar pseudo-atom refinement was carried out against 5417 observed data and the molecular electron density was analyzed using topological methods. The experimental electrostatic potential around the molecule is discussed in terms of molecular interactions. Crystal data: C6H12N2O4. 2H2O, Mr = 212.2, orthorhombic, P2(1)2(1)2(1), Z = 4, F(000) = 456 e, T = 110 K, a = 9.572 (3), b = 10.039 (3), c = 10.548 (2) A, V = 1013.6 (4) A3, Dx = 1.3 g cm(-3), mu = 1.2 cm(-1) for lambdaMo = 0.7107 A.

Molecular fragment electric moments derived from the fit of the experimental electrostatic potential. Application to the water molecule.

The electrostatic potential is a multicenter property that can be expressed as a sum of the contributions of electric moments located at each atomic site of a molecule. Independently of the model used to generate the electrostatic potential around the system, these atomic moments can be accurately obtained by the fit of this physical property outside the van der Waals envelop. However, the larger the system, the greater the number of parameters. In this study a way is proposed to reduce the number of centers in the representation of the electrostatic potential which becomes a sum of fragment contributions rather than atomic ones. A sample of six water molecules in different crystal environments was chosen to discuss the derived values of the electric moments referred to the molecular center of mass.

New Synthesis of trans-Disubstituted Cyclam Macrocycles – Elucidation of the Disubstitution Mechanism on the Basis of X-ray Data and Molecular Modeling

A new way to synthesize trans-disubstituted cyclam tetraazamacrocycles 1 is reported. The synthesis proceeds in three steps via the tricyclic 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane system 2, which can be selectively dialkylated and hydrolyzed under basic conditions to give the final product 1. An understanding of the reactivity, based on the X-ray experimental electrostatic potential and molecular modeling of the 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane macrotricycle, has permitted the elucidation of a new reaction pathway leading to the trans-disubstituted cyclam.

New Synthesis oftrans-Disubstituted Cyclam Macrocycles – Elucidation of the Disubstitution Mechanism on the Basis of X-ray Data and Molecular Modeling

A new way to synthesize trans-disubstituted cyclam tetraazamacrocycles 1 is reported. The synthesis proceeds in three steps via the tricyclic 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane system 2, which can be selectively dialkylated and hydrolyzed under basic conditions to give the final product 1. An understanding of the reactivity, based on the X-ray experimental electrostatic potential and molecular modeling of the 1,4,8,11-tetraazatricyclo[9.3.1.14,8]hexadecane macrotricycle, has permitted the elucidation of a new reaction pathway leading to the trans-disubstituted cyclam.

Vitamin C at 120 K: experimental and theoretical study of the charge density

Vitamin C is an extremely interesting molecule, not only for its important biological properties, but also for its crystal structure in which the formation of several hydrogen bonds plays an important role. We have collected X-ray diffraction data at −153°C up to sin θ/ λ=1.17 Å −1. The crystals do not undergo any phase transformation and the space group remains P2 1 with two independent molecules in the asymmetric unit. In the final difference Fourier map non-spherical electron density in the bonding regions was clearly indicated. A study by means of a multipole expansion of the electron density has been performed and the experimental electrostatic potential maps obtained. We have also computed the electron density by means of the crystal-orbital approach as coded in the program crystal95 [R. Dovesi et al., crystal95 User's Manual, University of Torino]. A complete ab initio conformational analysis of the isolated molecule has also been carried out at HF-SCF and density functional level, with reasonably large basis sets. The results of this analysis are: (i) vitamin C molecules are tightly bound in the crystal by a network of eight intermolecular H-bonds per molecule. The relative strength of these bonds is well accounted for by the experimental electrostatic potential. No relevant intramolecular interactions are present; (ii) crystal95 calculations give a value of 44 kcal mol −1 as the sublimation energy per mole of molecules, computed at correlated level with 6-21G(d,p) and Perdew 91 potential [J.P. Perdew and Y. Wang, Phys. Rev. B, 45 (1992) 13244; M. Causà and A. Zupan, Chem. Phys. Lett., 220 (1994) 145]; (iii) the crystal95 electron density maps are in good agreement with the experimental ones; (iv) the calculations on the isolated molecule reveal that the most stable conformers are different from the X-ray structure and are characterized by intramolecular H-bonds; the maximum energy difference among the 11 conformers taken into account is less than 6 kcal mol −1; (v) the NMR analysis in water reveals that the least populated side-chain conformation around bond C5–C6 is that found in our computed gas-phase conformers with the most folded-up side chain, which are indeed less prone to be solvated.

Modelling Electrostatic Potential from Experimentally Determined Charge Densities. II. Total Potential

Experimental electrostatic potential derived from X-ray diffraction data was used as a given physical property for the determination of atomic moments. The electrostatic potential is fitted against Buckingham moments expansion up to octupolar level. The estimation of the contribution of the aspherical part of the density to the electrostatic potential necessitates a judicious choice of the points grid around the system in order to get stability and reliability of the results. The net charges obtained by the fit to the electrostatic potential on a test crystal of the pseudo-peptide N-acetyl-α,β-dehydrophenylalanine methylamide are close to those derived from the electron-density refinements. The higher moments are related to the electron-density multipolar parameters.