scholarly journals Migrating hydrogen in 2,4,6-triaminopyrimidinium(1+) x hydrogen trioxofluorophosphate(−) x monohydrate/2,4,6-triaminopyrimidinium(2+)1–x trioxofluorophosphate(2–)1–x monohydrate (0.0 < x < 0.73) with changing temperature

2017 ◽  
Vol 73 (6) ◽  
pp. 1114-1124
Author(s):  
Irena Matulková ◽  
Jan Fábry ◽  
Ivan Němec ◽  
Ivana Císařová ◽  
Přemysl Vaněk
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Electron Density ◽  
Double Layers ◽  
Scanning Calorimetry ◽  
Electron Ring ◽  
Density Maps ◽  
Hydrogen Bond Pattern ◽  
Bonding Properties ◽  
The Difference

The data of the title structure of 2,4,6-triaminopyrimidinium(1+) x hydrogen trioxofluorophosphate(1−) x monohydrate/2,4,6-triaminopyrimidinium(2+)1−x trioxofluorophosphate(2−)1−x monohydrate (0.0 < x < 0.73), with the sum formula C4H11FN5O4P, were collected in 10 K intervals between 290 and 150 K, as well as at 100 K. The most interesting feature is the presence of a moderate though still strong O—H...N/O...H—N hydrogen bond. Its bridging H atom was found to be disordered over two positions in the temperature interval 290–220 K, with the larger occupation towards the O atom. The occupation in the latter position decreased with decreasing temperature, though not monotonously. At 210 K and below, the difference electron-density maps showed just one maximum which was closer to the N atom. Though difference scanning calorimetry (DSC) revealed no anomaly in the interval 303–93 K, the dependence of the length of the unit-cell axes b and c on temperature showed a kink in the slope at about 190 K. The N...O distance of the mentioned hydrogen bond or the occupational parameter of the electron density of the disordered H atom indicate less pronounced anomalies for the temperatures 270 and 230 K. The cation and the anion, as well as the water molecules, form layers which are parallel to (10\overline{1}) and which are interconnected by O—H...N (in the interval 290–220 K), N—H...O and O—H...O hydrogen bonds of moderate strength. The layers are arranged into centrosymmetric double layers in which the F atoms are directed outwards. The layers are interconnected by water–acid O—H...O hydrogen bonds, weak N—H...F interactions and π-electron ring...π-electron ring interactions. The dependence of P—F bond lengths on bonding properties of the trioxofluorophosphate or hydrogen trioxofluorophosphate anions is discussed. It has been recognized that a carbon-bonded F atom avoids participation in a hydrogen-bond pattern; however, this property seems to be also common to fluorine bonded to P, As and S, especially if an oxygen ligand is also present in a molecule. The deposited material contains an overview of the determined structures with trioxofluorophosphate or hydrogen trioxofluorophosphate anions.

scholarly journals Crystal structure of heptaguanidinium nonahydrogen bis[α-hexamolybdoplatinate(IV)] heptahydrate

2015 ◽  
Vol 71 (3) ◽  
pp. 268-271 ◽  
Author(s):  
Hea-Chung Joo ◽  
Ki-Min Park ◽  
Uk Lee
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Water Molecule ◽  
Electron Density ◽  
Title Compound ◽  
Rotation Axis ◽  
Acta Cryst ◽  
Density Maps ◽  
Guanidinium Salt

The title compound, (CH6N3)7H9[PtMo6O24]2·7H2O, containing the well-known Anderson-type heteropolyoxomolybdate, was obtained by recrystallization of its powdered guanidinium salt. The protonated O atoms in the polyanion were confirmed by electron-density maps, interpolyanion hydrogen bonds and bond-valance sums (BVS). The {[H4.5PtMo6O24]2}7−polyanion is the same as that already characterized in K7[H4.5PtMo6O24]2·11H2O [space groupP-1; Lee & Joo (2010).Acta Cryst.E66, i8–i9]. The heteropolyanions form inversion-generated dimers, {[H4.5PtMo6O24]2}7−, held together by each of the four μ3-O—H...μ1-O, two μ2-O—H...μ2-O hydrogen bonds and one centrosymmetric μ3-O—H—μ3-O hydrogen bond. The H atom of the centrosymmetric hydrogen bond is located on an inversion centre. One guanidinium ion and one water molecule are equally disordered about a twofold rotation axis.

Synergy among phase-refinement techniques in macromolecular crystallography

2017 ◽  
Vol 73 (11) ◽  
pp. 877-888 ◽  
Author(s):  
Maria Cristina Burla ◽  
Giovanni Luca Cascarano ◽  
Carmelo Giacovazzo ◽  
Giampiero Polidori
Keyword(s):  
Ab Initio ◽  
Electron Density ◽  
Molecular Model ◽  
Experimental Tests ◽  
Protein Chemistry ◽  
Sources Of Information ◽  
Density Maps ◽  
Structure Solution ◽  
Molecular Interpretation ◽  
The Difference

Ab initioand non-ab initiophasing methods are often unable to provide phases of sufficient quality to allow the molecular interpretation of the resulting electron-density maps. Phase extension and refinement is therefore a necessary step: its success or failure can make the difference between solution and nonsolution of the crystal structure. Today phase refinement is trusted to electron-density modification (EDM) techniques, and in practice to dual-space methods which try,viasuitable constraints in direct and in reciprocal space, to generate higher quality electron-density maps. The most popular EDM approaches, denoted here as mainstream methods, are usually part of packages which assist crystallographers in all of the structure-solution steps from initial phasing to the point where the molecular model perfectly fits the known features of protein chemistry. Other phase-refinement approaches that are based on different sources of information, denoted here as out-of-mainstream methods, are not frequently employed. This paper aims to show that mainstream and out-of-mainstream methods may be combined and may lead to dramatic advances in the present state of the art. The statement is confirmed by experimental tests using molecular-replacement, SAD–MAD andab initiotechniques.

Excess volumes of an alcohol + 1,2-dichloroethane

1981 ◽  
Vol 59 (14) ◽  
pp. 2210-2211 ◽  
Author(s):  
Nettem V. Choudary ◽  
Puligundla R. Naidu
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Binary Mixtures ◽  
Excess Volumes ◽  
Hydrogen Bond Interaction ◽  
Bond Interaction ◽  
Break Up ◽  
The Difference

Excess volumes for binary mixtures of 1,2-dichloroethane with n-propanol, n-butanol, n-pentanol, n-hexanol, n-heptanol, and n-octanol have been determined at 303.15 K. VE is positive over the whole range of composition in all the mixtures. However, it is noticed that the positive values of VE of mixtures of 1,2-dichloroethane with n-hexanol, n-heptanol, and n-octanol differ from those for the mixtures of 1,2-dichloroethane with corresponding alkanes. The difference has been explained in terms of the break up of hydrogen bonds, interstitial accommodation of 1,2-dichloroethane in alcohol aggregates, and possible hydrogen bond interaction of the type Cl … H—O between unlike molecules.

Revision of Ferroelastic Structures of n-Heptyl- and n-Octylammonium Dihydrogen Phosphate Crystals

1997 ◽  
Vol 53 (2) ◽  
pp. 272-279 ◽  
Author(s):  
J. Fábry ◽  
V. Petrícek ◽  
I. Císarová ◽  
J. Kroupa
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Structure Determination ◽  
Symmetry Operation ◽  
Double Layers ◽  
Dihydrogen Phosphate ◽  
Hydrogen Bond Acceptor ◽  
Space Group ◽  
Unit Cells ◽  
Pass Through

This study deals with the structure determination of C7H15NH3 +.H2PO4 − (C7ADP) and C8H17NH3 +.H2PO4 − (C8ADP). The samples used in this study were not subjected to a phase transition after they had been crystallized. Unlike a previous structure determination, weak reflections, now with indices h = 2n + 1, were included. This means that both structures are described in unit cells with the lattice parameters a twice as long as given previously. Both structures are quite similar; two double layers of dihydrogen phosphates, which are interconnected by hydrogen bonds (2.52–2.62 Å), pass through each unit cell. Alkylammonium groups interact with these dihydrogen phosphates via longer hydrogen bonds (>2.75 Å), while the rest of the aliphatic chains interact via van der Waals contacts. All H atoms were localized and no disorder of the H atoms was detected. Both structures described in the space group P121/n1 exhibit a reproducible ferroelastic switching. The hypothetical prototypic phase is orthorhombic with the space group number 60 P2/b21/n21/a. All atoms except two hydrogen species exist in pairs linked by the lost symmetry operations derived from the prototypic space group and are brought close to each other – up to 0.25 Å – under the action of them. Each of these two different H atoms is involved in an asymmetric hydrogen bond between an oxygen pair. Under the action of a lost symmetry operation each of these H atoms is displaced from one oxygen towards the other. Therefore, it is assumed that during the ferroelastic switching the jumps of these two hydrogen species take place between the pertinent hydrogen-bond acceptor and donor O atoms. Hence, these O atoms reverse their role as hydrogen-bond donors and acceptors during the ferroelastic switching.

Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data

2008 ◽  
Vol 41 (3) ◽  
pp. 592-599 ◽  
Author(s):  
Angela Altomare ◽  
Corrado Cuocci ◽  
Carmelo Giacovazzo ◽  
Anna Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Electron Density ◽  
Direct Methods ◽  
Large Set ◽  
Acta Cryst ◽  
Pattern Decomposition ◽  
Density Maps ◽  
Decomposition Procedure ◽  
Data Resolution ◽  
Current Electron ◽  
The Difference

Fourier syntheses providing electron density maps are usually affected by truncation effects due to the limited data resolution. A recent theoretical approach [Altomare, Cuocci, Giacovazzo, Kamel, Moliterni & Rizzi (2008).Acta Cryst.A64, 326–336] suggests that the resolution bias may be reduced by correcting the current electron density maps in accordance with the physics of the diffraction experiment. We have implemented the approach inEXPO2004[Altomare, Caliandro, Camalli, Cuocci, Giacovazzo, Moliterni & Rizzi (2004).J. Appl. Cryst.37, 1025–1028], a program devoted to the solution of crystal structures from powder data. The new algorithm was applied at the end of the direct methods modulus, to verify if the reduction of the resolution bias is able to improve the electron density maps and to provide additional power to direct methods. Application of this method to a large set of test structures indicates that resolution-bias correction often makes the difference between success and failure, and thus constitutes a new tool for reducing the dependence of modern crystallography on resolution effects. The chances of failure are expected to depend on the quality of the experimental data (e.g.the accuracy of the full-pattern decomposition procedure and the data resolution), on the size of the structure and on its chemical composition.

scholarly journals Synthesis, crystal structure and spectroscopic and Hirshfeld surface analysis of 4-hydroxy-3-methoxy-5-nitrobenzaldehyde

2020 ◽  
Vol 76 (2) ◽  
pp. 239-244 ◽  
Author(s):  
Vitomir Vusak ◽  
Darko Vusak ◽  
Kresimir Molcanov ◽  
Mestrovic Ernest
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Hydrogen Atoms ◽  
Scanning Calorimetry ◽  
Bond Forming ◽  
Compound C

The title compound, C8H7NO5, is planar with an r.m.s. deviation for all non-hydrogen atoms of 0.018 Å. An intramolecular O—H...O hydrogen bond involving the adjacent hydroxy and nitro groups forms an S(6) ring motif. In the crystal, molecules are linked by O—H...O hydrogen bonds, forming chains propagating along the b-axis direction. The chains are linked by C—H...O hydrogen bonds, forming layers parallel to the bc plane. The layers are linked by a further C—H...O hydrogen bond, forming slabs, which are linked by C=O...π interactions, forming a three-dimensional supramolecular structure. Hirshfeld surface analysis was used to investigate intermolecular interactions in the solid state. The molecule was also characterized spectroscopically and its thermal stability investigated by differential scanning calorimetry and by thermogravimetric analysis.

scholarly journals 2,4-Dimethylpyrido[1,2-a]pyrimidin-5-ium perchlorate

IUCrData ◽  
2016 ◽  
Vol 1 (10) ◽  
Author(s):  
Maciej Posel ◽  
Helen Stoeckli-Evans
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Double Layers ◽  
Rotation Axes ◽  
Molecular Salt

In the title molecular salt, C10H11N2 +·ClO4 −, the pyrido[1,2-a]pyrimidin-5-ium cation is planar, with an r.m.s. deviation of 0.027 Å for all 12 non-H atoms. The perchlorate anions are distributed over two twofold rotation axes; for one, three of the O atoms are disordered over two sites (occupancies of 1/2). In the crystal, the cations are linked via C—H...N hydrogen bonds, forming chains propagating along [001]. The chains are linked by a C—H...O hydrogen bond involving the non-disordered perchlorate anion, forming double layers parallel to the bc plane. These layers are linked by a number of weak C—H...O hydrogen bonds involving the disordered perchlorate anion, forming a three-dimensional framework.

scholarly journals Bifurcated Hydrogen Bonds and the Fold Switching of Lymphotactin

2020 ◽  
Author(s):  
Prabir Khatua ◽  
Alan J Ray ◽  
Ulrich H. E. Hansmann
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Replica Exchange ◽  
Biological Functions ◽  
Physiological Conditions ◽  
Hydrogen Bond Pattern

AbstractLymphotactin (Ltn) exists under physiological conditions in an equilibrium between two interconverting structures with distinct biological functions. Using Replica-Exchange-with-Tunneling we study the conversion between the two folds. Unlike previously proposed, we find that the fold switching does not require unfolding of Lymphotactin, but proceeds through a series of intermediates that remain partially structured. This process relies on two bifurcated hydrogen bonds that connect the β2 and β3 strands and eases the transition between the hydrogen bond pattern by which the central three-stranded β-sheet in the two forms differ.

Hydrogen Bonding Contribution to Lipophilicity Parameters. Hydrogen Acceptor and Hydrogen Acceptor Donor Parameters

2004 ◽  
Vol 69 (12) ◽  
pp. 2147-2173 ◽  
Author(s):  
Marvin Charton ◽  
Barbara I. Charton
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Reasonable Assumption ◽  
Hydrogen Acceptor ◽  
Donor Capacity ◽  
The Difference ◽  
Acceptor Capacity ◽  
Lipophilicity Parameters ◽  
Hydrogen Bond Energies

In our analysis of the composition of lipophilicity parameters by the intermolecular force (IMF) model we have made use of nH, the number of OH and/or NH bonds, as a measure of the hydrogen donor capacity of a substituent; and nn, the number of lone pairs on O and/or N atoms in the substituent, as a measure of the hydrogen acceptor capacity of the substituent. The basis of this method is the reasonable assumption that in 55.6 molar water hydrogen bonding is maximized. The method does not account however for differences in the energy of different types of hydrogen bonds, but further assumes that these differences are to a first approximation negligible. In order to improve the model we have defined a scale of group hydrogen bonding acceptor parameters, ηXHA, and overall hydrogen bond parameters ηXHAD from the water/1-octanol partition coefficients of AkX where Ak is alkyl. These parameters should account for both the extent of hydrogen bonding in water and for the difference in hydrogen bond energies of the various types of hydrogen bonds encountered. Correlations of log P values for Ph(CH2)nX, X1(CH2)X2, and substituted amino acids Xaa with the IMF equation using the ηXHA and ηXHAD parameters demonstrated their use. Correlation of log P values for PhX suggested that for many groups separate sets of ηXHA and ηXHAD values are required when they are bonded to sp2 hybridized carbon rather than sp3 hybridized carbon.

scholarly journals Statistical quality indicators for electron-density maps

2012 ◽  
Vol 68 (4) ◽  
pp. 454-467 ◽  
Author(s):  
Ian J. Tickle
Keyword(s):  
Electron Density ◽  
Statistical Significance ◽  
Significance Test ◽  
Real Space ◽  
Structure Model ◽  
Space Correlation ◽  
The Real ◽  
Difference Density ◽  
Density Maps ◽  
The Difference

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ2 significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

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