Pub Date : 2017-12-01DOI: 10.1107/S2052520617014007
I. Matulková, J. Fábry, I. Němec, I. Císařová, P. Vanĕk
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 (10overline{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.
{"title":"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","authors":"I. Matulková, J. Fábry, I. Němec, I. Císařová, P. Vanĕk","doi":"10.1107/S2052520617014007","DOIUrl":"https://doi.org/10.1107/S2052520617014007","url":null,"abstract":"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 (10overline{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.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"18 1","pages":"1114-1124"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84151871","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617012689
S. Volkov, M. Dušek, R. Bubnova, M. Krzhizhanovskaya, V. Ugolkov, E. Obozova, S. Filatov
Crystal structures of γ-, β- and α-Sr2B2O5 polymorphs resulting from the γ ↔ (at 565 K) β ↔ (at 637 K) α′ ↔ (at 651 K) α sequence of reversible first-order phase transitions are studied by high-temperature single-crystal X-ray diffraction, high-temperature X-ray powder diffraction, differential scanning calorimetry and impedance spectroscopy. Out of these phases, the structure of γ-Sr2B2O5 was already known whereas the structures of β- and α-Sr2B2O5 were determined for the first time. The sequence of phase transitions is associated with an unusual change of symmetry, with triclinic intermediate β-Sr2B2O5 phase and monoclinic low-temperature γ-Sr2B2O5 as well as high-temperature α-Sr2B2O5 phase. Taking the α-Sr2B2O5 phase with space group P21/c as a parent structure, the γ-Sr2B2O5 phase was refined as a twofold superstructure with symmetry P21/c, whereas the β-Sr2B2O5 phase was a sixfold superstructure with symmetry P{overline 1}. To construct a unified structure model for all Sr2B2O5 modifications, phases of γ- and β-Sr2B2O5 were also refined as commensurately modulated structures using the basic unit cell of the parent α-Sr2B2O5. The phase transitions are related to the orientational order–disorder arrangement of B2O5 pyroborate groups, where the degree of disorder grows towards the high-temperature phase. Thermal expansion is strongly anisotropic and dictated by preferable orientations of BO3 triangles in the structure. The intermediate phase α′-Sr2B2O5, stable over a narrow temperature range (637–651 K), features the largest anisotropy of expansion for the known borates: α11 = 205, α22 = 57, α33 = −81 × 10−6 K−1.
{"title":"Orientational order-disorder γ ↔ β ↔ α′ ↔ α phase transitions in Sr2B2O5 pyroborate and crystal structures of β and α phases","authors":"S. Volkov, M. Dušek, R. Bubnova, M. Krzhizhanovskaya, V. Ugolkov, E. Obozova, S. Filatov","doi":"10.1107/S2052520617012689","DOIUrl":"https://doi.org/10.1107/S2052520617012689","url":null,"abstract":"Crystal structures of γ-, β- and α-Sr2B2O5 polymorphs resulting from the γ ↔ (at 565 K) β ↔ (at 637 K) α′ ↔ (at 651 K) α sequence of reversible first-order phase transitions are studied by high-temperature single-crystal X-ray diffraction, high-temperature X-ray powder diffraction, differential scanning calorimetry and impedance spectroscopy. Out of these phases, the structure of γ-Sr2B2O5 was already known whereas the structures of β- and α-Sr2B2O5 were determined for the first time. The sequence of phase transitions is associated with an unusual change of symmetry, with triclinic intermediate β-Sr2B2O5 phase and monoclinic low-temperature γ-Sr2B2O5 as well as high-temperature α-Sr2B2O5 phase. Taking the α-Sr2B2O5 phase with space group P21/c as a parent structure, the γ-Sr2B2O5 phase was refined as a twofold superstructure with symmetry P21/c, whereas the β-Sr2B2O5 phase was a sixfold superstructure with symmetry P{overline 1}. To construct a unified structure model for all Sr2B2O5 modifications, phases of γ- and β-Sr2B2O5 were also refined as commensurately modulated structures using the basic unit cell of the parent α-Sr2B2O5. The phase transitions are related to the orientational order–disorder arrangement of B2O5 pyroborate groups, where the degree of disorder grows towards the high-temperature phase. Thermal expansion is strongly anisotropic and dictated by preferable orientations of BO3 triangles in the structure. The intermediate phase α′-Sr2B2O5, stable over a narrow temperature range (637–651 K), features the largest anisotropy of expansion for the known borates: α11 = 205, α22 = 57, α33 = −81 × 10−6 K−1.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"80 1","pages":"1056-1067"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91142266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617012525
H. Jenkins, A. Vegas
This article examines the comparison between the classical formulations used to describe silicates and that derived from the application of the extended Zintl– Klemm concept (EZKC). The ionic strength, I, for 25 silicate lattices is calculated taking into account both formulations, and the results show that, in every single one of the examples, the ionic strength of the Zintl polyanion is higher than that of the classical model which assigns a formal charge of 4+ for silicon. Our earlier study, firstly applied to the germanate (NH4)2Ge [Ge6O15] [Vegas & Jenkins (2017). Acta Cryst. B73, 94–100] and to the polyanion [Ge6O15] 6 equivalent to the pseudo-As2O5 derived from it, explained satisfactorily the charge transfer that takes place in the Zintl compounds. The value of I = 12 P nizi 2 for the Zintl polyanion was greater than for the compound as formulated in the classical way. In that article, a meaningful relationship was found between the electron transfers as defined by the EZKC and the ionic strength I of the anion [Ge6O15] 6 -As2O5. Because the ionic strength, I, of a lattice is directly proportional to the lattice potential energy, UPOT, the higher the I the greater the UPOT; thus it is harder to break up the lattice into its constituent ions and hence the lattice itself is more stable, giving support to the idea that the application of the EZKC and the resulting electron shifts yields structures which are inherently thermodynamically more stable than the starting configuration.
{"title":"The extended Zintl–Klemm concept, ionic strength I and assessment of the relative stability of lattices using the stability enhancement ratio S","authors":"H. Jenkins, A. Vegas","doi":"10.1107/S2052520617012525","DOIUrl":"https://doi.org/10.1107/S2052520617012525","url":null,"abstract":"This article examines the comparison between the classical formulations used to describe silicates and that derived from the application of the extended Zintl– Klemm concept (EZKC). The ionic strength, I, for 25 silicate lattices is calculated taking into account both formulations, and the results show that, in every single one of the examples, the ionic strength of the Zintl polyanion is higher than that of the classical model which assigns a formal charge of 4+ for silicon. Our earlier study, firstly applied to the germanate (NH4)2Ge [Ge6O15] [Vegas & Jenkins (2017). Acta Cryst. B73, 94–100] and to the polyanion [Ge6O15] 6 equivalent to the pseudo-As2O5 derived from it, explained satisfactorily the charge transfer that takes place in the Zintl compounds. The value of I = 12 P nizi 2 for the Zintl polyanion was greater than for the compound as formulated in the classical way. In that article, a meaningful relationship was found between the electron transfers as defined by the EZKC and the ionic strength I of the anion [Ge6O15] 6 -As2O5. Because the ionic strength, I, of a lattice is directly proportional to the lattice potential energy, UPOT, the higher the I the greater the UPOT; thus it is harder to break up the lattice into its constituent ions and hence the lattice itself is more stable, giving support to the idea that the application of the EZKC and the resulting electron shifts yields structures which are inherently thermodynamically more stable than the starting configuration.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"1 1","pages":"1051-1055"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89238514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617012057
C. Czech, J. Glinnemann, K. E. Johansson, M. Bolte, M. Schmidt
dl-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases ( , , ). The crystal structure of the -phase was redetermined at 173 K. Diffraction patterns of the and -phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersioncorrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the -phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.
dl-去甲亮氨酸(2-氨基己酸，C6H13NO2)在所有已知相中均为双层结构(，，)。在173 K时重新测定了-相的晶体结构。和-相的衍射图经常显示平行于c*的漫射条纹，这表明层的堆叠无序。通过对称分析，推导出可能的叠加顺序。利用力场和色散校正密度泛函理论(DFT-D)对Z = 4、8和16、不同堆叠顺序的有序模型结构进行格能最小化。计算得到的能量不仅与相邻双层的排列有关，还与相邻双层的排列有关。根据DFT-D能量计算叠加概率。根据计算的叠加概率，构建了包含100层双层的大型模型。他们的模拟衍射图显示出h + k = 2n时的清晰反射和h + k = 2n + 1时平行于c*的漫射条纹。实验单晶x射线衍射结果表明，在173 K时，去甲亮氨酸存在于-相中，并存在无序堆叠。再加热至室温后，所研究的晶体在h + k = 2n + 1的条件下，通过所有反射显示出与c*平行的强漫射散射衍射图样，这与模拟的无序结构吻合较好。
{"title":"On the stacking disorder of dl‐norleucine","authors":"C. Czech, J. Glinnemann, K. E. Johansson, M. Bolte, M. Schmidt","doi":"10.1107/S2052520617012057","DOIUrl":"https://doi.org/10.1107/S2052520617012057","url":null,"abstract":"dl-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases ( , , ). The crystal structure of the -phase was redetermined at 173 K. Diffraction patterns of the and -phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersioncorrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the -phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"231 1","pages":"1075-1084"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89248445","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617014044
H. Kasai, Lirong Song, H. L. Andersen, H. Yin, B. Iversen
A multi-temperature structural study of Mg2Si and Mg2Sn was carried out from 100 to 700 K using synchrotron X-ray powder diffraction. The temperature dependence of the lattice parameters can be expressed as a = 6.3272 (4) + 6.5 (2) × 10−5T + 4.0 (3) × 10−8T2 A and a = 6.7323 (7) + 8.5 (4) × 10−5T + 3.8 (5) × 10−8T2 A for Mg2Si and Mg2Sn, respectively. The atomic displacement parameters (ADPs) are reported and analysed using a Debye model for the averaged Uiso giving Debye temperatures of 425 (2) K for Mg2Si and 243 (2) K for Mg2Sn. The ADPs are considerably smaller for Mg2Si than for Mg2Sn reflecting the weaker chemical bonding in the Mg2Sn structure. Following the heating, an annealing effect is observed on the lattice parameters and peak widths in both structures, presumably due to changes in the crystal defects, but the lattice thermal expansion is almost unchanged by the annealing. This work provides accurate structural parameters which are of importance for studies of Mg2Si, Mg2Sn and their solid solutions.
{"title":"Multi‐temperature structure of thermoelectric Mg2Si and Mg2Sn","authors":"H. Kasai, Lirong Song, H. L. Andersen, H. Yin, B. Iversen","doi":"10.1107/S2052520617014044","DOIUrl":"https://doi.org/10.1107/S2052520617014044","url":null,"abstract":"A multi-temperature structural study of Mg2Si and Mg2Sn was carried out from 100 to 700 K using synchrotron X-ray powder diffraction. The temperature dependence of the lattice parameters can be expressed as a = 6.3272 (4) + 6.5 (2) × 10−5T + 4.0 (3) × 10−8T2 A and a = 6.7323 (7) + 8.5 (4) × 10−5T + 3.8 (5) × 10−8T2 A for Mg2Si and Mg2Sn, respectively. The atomic displacement parameters (ADPs) are reported and analysed using a Debye model for the averaged Uiso giving Debye temperatures of 425 (2) K for Mg2Si and 243 (2) K for Mg2Sn. The ADPs are considerably smaller for Mg2Si than for Mg2Sn reflecting the weaker chemical bonding in the Mg2Sn structure. Following the heating, an annealing effect is observed on the lattice parameters and peak widths in both structures, presumably due to changes in the crystal defects, but the lattice thermal expansion is almost unchanged by the annealing. This work provides accurate structural parameters which are of importance for studies of Mg2Si, Mg2Sn and their solid solutions.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"67 1","pages":"1158-1163"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74803017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617016572
U. Müller
According to the Preface, ‘the book aims to be useful for undergraduates’, and its title and the list of contents give the impression that this is a textbook for advanced students of chemistry. But that is not the case. Essential concepts of crystal chemistry are not covered at all, such as ionic radius ratios, Pauling’s rules, lattice energy, phase diagrams and chemical bonding in solids. Some classes of compounds such as silicates, intermetallics and Zintl phases are completely missing. The conception is not a general building up of knowledge in crystal chemistry, but a notional view at coordination polyhedra and their joining with increasing complexity, reflecting predilections of the author and culminating in results of the author’s research. It is inconsistent that some basic crystallographic terms are explained, such as rotations, rotoinversions, screw rotations and glide reflections, while other crystallographic topics are expected to be known. The terms ‘symmetry operation’ and ‘symmetry element’ are used frequently, but not explained, and sometimes confused. Crystallographic group theory, cell settings and cell transformations are not a subject. Point groups and their symbols are not really explained and it is (wrongly) claimed that their number is restricted to 32. Space groups, Hermann–Mauguin symbols and Miller indices are explained in a rather terse way. Rotation axes are termed A2, A3, . . . and rotoinversion axes A 3, A 4, . . . in lieu of the usual symbols. The use of mathematics is restricted to the calculation of interatomic distances. Chapter 1 begins with Platonic and Archimedean polyhedra and how they are joined in simple crystal structures (detailed geometric data follow in an appendix). The primitive cubic packing and the close-packings of spheres are explained together with their interstices. An approach that is repeatedly used throughout the book is to insert atoms at the points of contact of the spheres; this is called a decoration or a substitution of joined polyhedra for spheres, ‘keeping the topology’. ‘Topology’ is the all-dominant term in the book, and yet never explained, now and then ambiguous and not quite in accordance with its mathematical definition. The elaborate Chapter 3 (45 pages) gives instructions on how to interpret perspective drawings, projections and crystal data (lattice parameters, atomic coordinates including symmetry-equivalent positions). This illuminating chapter begins with a lengthy explanation of the rutile structure, which is described as a distorted hexagonal arrangement of ‘oxygens’ with octahedral interstices occupied by Ti atoms. It is not mentioned that the packing of the oxygen atoms is a tetragonal close packing with the coordination number 11. The structure types of CaF2, NaCl, NiAs, cubic and hexagonal ZnS, -Al2O3, -Ga2O3, CdCl2, CdI2, MgAl2O4 (spinel), K2NiF4, ReO3, MoO3, tungsten bronzes and several others are explained in detail. That includes their space groups, lattice paramet
{"title":"Crystal Chemistry. From Basics to Tools for Materials Creation. By Gérard Ferey. World Scientific, 2017, 264 pp. Softcover ISBN 978-981-3144-19-4, price GBP 46.00, hardback, ISBN 978-981-3144-18-7, price GBP 81.00","authors":"U. Müller","doi":"10.1107/S2052520617016572","DOIUrl":"https://doi.org/10.1107/S2052520617016572","url":null,"abstract":"According to the Preface, ‘the book aims to be useful for undergraduates’, and its title and the list of contents give the impression that this is a textbook for advanced students of chemistry. But that is not the case. Essential concepts of crystal chemistry are not covered at all, such as ionic radius ratios, Pauling’s rules, lattice energy, phase diagrams and chemical bonding in solids. Some classes of compounds such as silicates, intermetallics and Zintl phases are completely missing. The conception is not a general building up of knowledge in crystal chemistry, but a notional view at coordination polyhedra and their joining with increasing complexity, reflecting predilections of the author and culminating in results of the author’s research. It is inconsistent that some basic crystallographic terms are explained, such as rotations, rotoinversions, screw rotations and glide reflections, while other crystallographic topics are expected to be known. The terms ‘symmetry operation’ and ‘symmetry element’ are used frequently, but not explained, and sometimes confused. Crystallographic group theory, cell settings and cell transformations are not a subject. Point groups and their symbols are not really explained and it is (wrongly) claimed that their number is restricted to 32. Space groups, Hermann–Mauguin symbols and Miller indices are explained in a rather terse way. Rotation axes are termed A2, A3, . . . and rotoinversion axes A 3, A 4, . . . in lieu of the usual symbols. The use of mathematics is restricted to the calculation of interatomic distances. Chapter 1 begins with Platonic and Archimedean polyhedra and how they are joined in simple crystal structures (detailed geometric data follow in an appendix). The primitive cubic packing and the close-packings of spheres are explained together with their interstices. An approach that is repeatedly used throughout the book is to insert atoms at the points of contact of the spheres; this is called a decoration or a substitution of joined polyhedra for spheres, ‘keeping the topology’. ‘Topology’ is the all-dominant term in the book, and yet never explained, now and then ambiguous and not quite in accordance with its mathematical definition. The elaborate Chapter 3 (45 pages) gives instructions on how to interpret perspective drawings, projections and crystal data (lattice parameters, atomic coordinates including symmetry-equivalent positions). This illuminating chapter begins with a lengthy explanation of the rutile structure, which is described as a distorted hexagonal arrangement of ‘oxygens’ with octahedral interstices occupied by Ti atoms. It is not mentioned that the packing of the oxygen atoms is a tetragonal close packing with the coordination number 11. The structure types of CaF2, NaCl, NiAs, cubic and hexagonal ZnS, -Al2O3, -Ga2O3, CdCl2, CdI2, MgAl2O4 (spinel), K2NiF4, ReO3, MoO3, tungsten bronzes and several others are explained in detail. That includes their space groups, lattice paramet","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"45 1","pages":"1198-1199"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74169759","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617014731
M. Buděšínský, I. Císařová, F. Borremans, J. Martins, E. Pauwels
Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the β, γ or δ position) or thia-proline (with sulfur in the β or γ position) and N-methyl phenylalanine [(NMe)Phe]: cyclo[(β-S)Pip-(NMe)Phe], cyclo[(γ-S)Pip-(NMe)Phe], cyclo[(δ-S)Pip-(NMe)Phe], cyclo[(β-S)Pro-(NMe)Phe] and cyclo[(γ-S)Pro-(NMe)Phe] were determined with X-ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H⋯O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non-planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell (Z′ > 1), though in some cases a correlation is observed.
{"title":"Solid‐state structure of cyclic dipeptides: an X‐ray and computational study of cis‐ and trans‐diketopiperazines of N‐methyl‐phenylalanine with the thia‐pipecolic acids and thia‐prolines","authors":"M. Buděšínský, I. Císařová, F. Borremans, J. Martins, E. Pauwels","doi":"10.1107/S2052520617014731","DOIUrl":"https://doi.org/10.1107/S2052520617014731","url":null,"abstract":"Ten new crystal structures of cis and trans bicyclic diketopiperazines (DKPs) of thia-pipecolic acid (with sulfur in the β, γ or δ position) or thia-proline (with sulfur in the β or γ position) and N-methyl phenylalanine [(NMe)Phe]: cyclo[(β-S)Pip-(NMe)Phe], cyclo[(γ-S)Pip-(NMe)Phe], cyclo[(δ-S)Pip-(NMe)Phe], cyclo[(β-S)Pro-(NMe)Phe] and cyclo[(γ-S)Pro-(NMe)Phe] were determined with X-ray crystallography. Density functional theory calculations of these molecules in the gas phase succeed in reproducing the observed molecular conformations in the crystal remarkably well. This illustrates the weak to moderate impact of intermolecular packing forces in the absence of classical N—H⋯O hydrogen bonds. The effect of sulfur on the geometry of the DKP ring and details of amide bond non-planarity are discussed. Molecular flexibility of the DKP ring, as estimated from the calculated deformation energies of its endocyclic ring torsion angles, is not in general the decisive factor for the occurrence of multiple symmetry independent molecules in the unit cell (Z′ > 1), though in some cases a correlation is observed.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"7 1","pages":"1179-1193"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80387730","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617011131
A. Vegas, H. Jenkins
Taking into account new experimental data [Barkalov et al. (2016). Solid State Sci. 61, 220–224] on the pressure-induced Ni2In phase of Li2S, at 30 GPa, three concepts related to high-pressure phase transitions are reviewed here. This paper firstly reviews evidence that chemical oxidation (by inclusion of oxygen atoms) can produce a similar effect to the application of physical high pressure and temperature, in an effect labelled as the oxidation–pressure concept. Secondly, the pressure-induced Ni2In phase of Li2S is the final phase in the double transition antifluorite → anticotunnite → Ni2In, as is observed in other alkali metal sulfides. This new phase for Li2S could be expected after knowledge of the high-pressure Cmcm phase of Li2SO4, which is a distortion of the hexagonal I-Na2SO4 phase, both having M2S subarrays of the Ni2In-type. Thirdly, in order to clarify these links, a simple methodology is proposed for gauging the level of increased stability (by defining a stability enhancement ratio, S) when the extended Zintl–Klemm concept (EZKC) has been applied. The method uses relative values of the lattice potential energies estimated for Li2S and for the pseudo-lattice Ψ-BeS derived by applying the EZKC to Li2S, after which, Li2S can be reformulated as Li+[LiS]− ≡ Li+[Ψ-BeS].
考虑到新的实验数据[Barkalov et al.(2016)]。本文对高压相变的三个相关概念进行了综述。固体科学，61,220-224]。本文首先回顾了化学氧化(通过包含氧原子)可以产生与物理高压和高温应用类似的效果的证据，这种效果被称为氧化压力概念。其次，与其他碱金属硫化物一样，Li2S的压力诱导Ni2In相是反萤石→反钙隧矿→Ni2In双过渡的最终相。在了解Li2SO4的高压Cmcm相之后，Li2S的这种新相是可以预期的，Li2SO4的高压Cmcm相是六边形I-Na2SO4相的一种变形，两者都具有ni2in型的M2S亚阵列。第三，为了澄清这些联系，当应用扩展的Zintl-Klemm概念(EZKC)时，提出了一种简单的方法来衡量增加的稳定性水平(通过定义稳定性增强比S)。该方法使用通过将EZKC应用于Li2S而得到的Li2S和伪晶格Ψ-BeS的晶格势能的相对值，之后，Li2S可以被重新表示为Li+[LiS]−≡Li+[Ψ-BeS]。
{"title":"A review of the oxidation–pressure concept (OPC) and extended Zintl–Klemm concept (EZKC), and the emergence of the high‐pressure Ni2In‐type phase of lithium sulfide (Li2S) rationalized by reference to a newly defined stability enhancement ratio (S)","authors":"A. Vegas, H. Jenkins","doi":"10.1107/S2052520617011131","DOIUrl":"https://doi.org/10.1107/S2052520617011131","url":null,"abstract":"Taking into account new experimental data [Barkalov et al. (2016). Solid State Sci. 61, 220–224] on the pressure-induced Ni2In phase of Li2S, at 30 GPa, three concepts related to high-pressure phase transitions are reviewed here. This paper firstly reviews evidence that chemical oxidation (by inclusion of oxygen atoms) can produce a similar effect to the application of physical high pressure and temperature, in an effect labelled as the oxidation–pressure concept. Secondly, the pressure-induced Ni2In phase of Li2S is the final phase in the double transition antifluorite → anticotunnite → Ni2In, as is observed in other alkali metal sulfides. This new phase for Li2S could be expected after knowledge of the high-pressure Cmcm phase of Li2SO4, which is a distortion of the hexagonal I-Na2SO4 phase, both having M2S subarrays of the Ni2In-type. Thirdly, in order to clarify these links, a simple methodology is proposed for gauging the level of increased stability (by defining a stability enhancement ratio, S) when the extended Zintl–Klemm concept (EZKC) has been applied. The method uses relative values of the lattice potential energies estimated for Li2S and for the pseudo-lattice Ψ-BeS derived by applying the EZKC to Li2S, after which, Li2S can be reformulated as Li+[LiS]− ≡ Li+[Ψ-BeS].","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"15 1","pages":"1043-1050"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79096473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-12-01DOI: 10.1107/S2052520617011490
Benjamin M Ridgway, Ana Foi, R. Corrêa, D. Bikiel, J. Ellena, F. Doctorovich, F. D. Salvo
Transition metal complexes containing dimethyl sulfoxide (DMSO) are important precursors in catalysis and metallodrugs. Understanding the solid-state supramolecular structure is crucial for predicting the properties and biological activity of the material. Several crystalline phases of DMSO-coordinated iridium anions with different cations, potassium (1a) and n-butylammonium (1b), were obtained and their structures determined by X-ray crystallography. Compound (1a) is present in two solvatomorphic forms: α and β; the β form contains disordered solvent water. In addition, the structures exhibit different rotamers of the trans-[IrCl4(DMSO)2]− anion with the trans-DMSO ligands being oriented in anti and gauche conformations. In consideration of these various conformers, the effects of the crystallized solvent and intermolecular interactions on the conformational preferences of the anion are discussed. In addition, density functional theory calculations were used to investigate the energies of the anions in the different conformations. It was found that hydrogen bonds between water and the DMSO complex stabilize the gauche conformation which is the least stable form of the trans-DMSO complex. Consequently, by controlling the number of hydrogen-bond donors and acceptors and the amount of water, it may be possible to obtain different solvatomorphs of clinically significant metallodrugs.
{"title":"Conformational and structural diversity of iridium dimethyl sulfoxide complexes","authors":"Benjamin M Ridgway, Ana Foi, R. Corrêa, D. Bikiel, J. Ellena, F. Doctorovich, F. D. Salvo","doi":"10.1107/S2052520617011490","DOIUrl":"https://doi.org/10.1107/S2052520617011490","url":null,"abstract":"Transition metal complexes containing dimethyl sulfoxide (DMSO) are important precursors in catalysis and metallodrugs. Understanding the solid-state supramolecular structure is crucial for predicting the properties and biological activity of the material. Several crystalline phases of DMSO-coordinated iridium anions with different cations, potassium (1a) and n-butylammonium (1b), were obtained and their structures determined by X-ray crystallography. Compound (1a) is present in two solvatomorphic forms: α and β; the β form contains disordered solvent water. In addition, the structures exhibit different rotamers of the trans-[IrCl4(DMSO)2]− anion with the trans-DMSO ligands being oriented in anti and gauche conformations. In consideration of these various conformers, the effects of the crystallized solvent and intermolecular interactions on the conformational preferences of the anion are discussed. In addition, density functional theory calculations were used to investigate the energies of the anions in the different conformations. It was found that hydrogen bonds between water and the DMSO complex stabilize the gauche conformation which is the least stable form of the trans-DMSO complex. Consequently, by controlling the number of hydrogen-bond donors and acceptors and the amount of water, it may be possible to obtain different solvatomorphs of clinically significant metallodrugs.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"2 1","pages":"1032-1042"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84254179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2017-03-14DOI: 10.1107/S2052520617013646
R. Federicci, B. Baptiste, F.Finocchi, A. Popa, L. Brohan, K. Béneut, P. Giura, G. Rousse, A. Descamps‐Mandine, T. Douillard, A. Shukla, B. Léridon
Recent results have demonstrated an exceptionally high permittivity in the range 200–330 K in crystalline titanium oxide Rb2Ti2O5. In this article, the possibility of a structural transition giving rise to ferroelectricity is carefully inspected. In particular, X-ray diffraction, high-resolution transmission electron microscopy and Raman spectroscopy are performed. The crystal structure is shown to remain invariant and centrosymmetric at all temperatures between 90 K and 450 K. The stability of the C2/m structure is confirmed by density functional theory calculations. These important findings allow the existence of a conventional ferroelectric phase transition to be ruled out as a possible mechanism for the colossal permittivity and polarization observed in this material.
{"title":"The crystal structure of Rb2Ti2O5","authors":"R. Federicci, B. Baptiste, F.Finocchi, A. Popa, L. Brohan, K. Béneut, P. Giura, G. Rousse, A. Descamps‐Mandine, T. Douillard, A. Shukla, B. Léridon","doi":"10.1107/S2052520617013646","DOIUrl":"https://doi.org/10.1107/S2052520617013646","url":null,"abstract":"Recent results have demonstrated an exceptionally high permittivity in the range 200–330 K in crystalline titanium oxide Rb2Ti2O5. In this article, the possibility of a structural transition giving rise to ferroelectricity is carefully inspected. In particular, X-ray diffraction, high-resolution transmission electron microscopy and Raman spectroscopy are performed. The crystal structure is shown to remain invariant and centrosymmetric at all temperatures between 90 K and 450 K. The stability of the C2/m structure is confirmed by density functional theory calculations. These important findings allow the existence of a conventional ferroelectric phase transition to be ruled out as a possible mechanism for the colossal permittivity and polarization observed in this material.","PeriodicalId":6887,"journal":{"name":"Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry","volume":"79 1","pages":"1142-1150"},"PeriodicalIF":0.0,"publicationDate":"2017-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76841485","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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