Bond length and radii variations in fluoride and oxide molecules and crystals

Molecular orbital calculations completed on fluoride molecules containing first and second row cations have generated bond lengths, R, that match those observed for coordinated polyhedra in crystals to within ～0.04 Å, on average. The calculated bond lengths and those observed for fluoride crystals can be ranked with the expression R=Kp ^?0.22, where p=s/r, s is the Pauling strength of the bond, r is the row number of the cation and K=1.34. The exponent -0.22 (≈ -2/9) is the same as that observed for oxide, nitride and sulfide molecules and crystals. Bonded radii for the fluoride anion, obtained from theoretical electron density maps, increase linearly with bond length. Those calculated for the cations as well as for the fluoride anion match calculated promolecule radii to within ～0.03 Å, on average, suggesting that the electron density distributions in the vicinity of the minima along the bond paths possess a significant atomic component despite bond type. Bonded radii for Si and O ions provided by experimental electron density maps measured for the oxides coesite, danburite and stishovite match those calculated for a series of monosilicic acid molecules. The resulting radii increase with bond length and coordination number with the radius of the oxide ion increasing at a faster rate than that of the Si cation. The oxide ion within danburite exhibits several distinct radii, ranging between 0.9 and 1.2 Å, rather than a single radius with each exhibiting a different radius along each of the nonequivalent bonds with B, Si and Ca. Promolecule radii calculated for the coordinated polyhedra in danburite match procrystal radii obtained in a structure analysis to within 0.002 Å. The close agreement between these two sets of radii and experimentally determined bonded radii lends credence to Slater's statement that the difference between the electron density distribution observed for a crystal and that calculated for a procrystal (IAM) model of the crystal “would be small and subtle, and very hard to determine by examination of the total charge density.”     

SiO bonded interactions in coesite: a comparison of crystalline, molecular and experimental electron density distributions

Bond critical point properties of electron density distributions calculated for representative Si₅O₁₆ moieties of the structure of coesite are compared with those observed and calculated for the bulk crystal. The values calculated for the moieties agree with those observed to within ∼5%, on average, whereas those calculated for the crystal agree to within ∼10%. As the SiOSi angles increase and the SiO bonds shorten, there is a progressive build-up in the calculated electron density along the bonds. This is accompanied by an increase in both the curvatures of the electron density, both perpendicular and parallel to each bond, and the Laplacian of the electron density distribution at the bond critical points. The cross sections of the bonds at the critical points become more circular as the angle approaches 180o. Also, the bonded radius of the oxide anion decreases about twice as much as that of the Si cation as the SiO bond length decreases and the fraction of s-character of the bond is indicated to increase. A knowledge of electron density distributions is central to our understanding of the forces that govern the structure, properties, solid state reactions, surface reactions and phase transformations of minerals. The software (CRYSTAL95 and TOPOND) used in this study to calculate the bond critical properties of the electron density and Laplacian distributions is bound to promote a deeper understanding of crystal chemistry and properties. Received: 23 February 1998 / Revised, accepted: 16 July 1998     

Power law relationships between bond length, bond strength and electron density distributions

The strength of a bond, defined as p=s/r, where s is the Pauling bond strength and r is the row number of an M cation bonded to an oxide anion, is related to a build-up of electron density along the MO bonds in a relatively large number of oxide and hydroxyacid molecules, three oxide minerals and three molecular crystals. As p increases, the value of the electron density is observed to increase at the bond critical points with the lengths of the bonds shortening and the electronegativities of the M cations bonded to the oxide anion increasing. The assertion that the covalency of a bond is intrinsically connected to its bond strength is supported by the electron density distribution and its bond critical point properties. A connection also exists between the properties of the electron density distributions and the connectivity of the bond strength network formed by the bonded atoms of a structure. Received: 20 August 1997 / Revised, accepted: 3 November 1997     

Atomic and ionic radii: a comparison with radii derived from electron density distributions

 The bonded radii of anions obtained in topological analyses of theoretical and experimental electron density distributions differ from atomic, ionic and crystal radii in that oxide-, fluoride-, nitride- and sulfide-anion radii are not constant for a given coordination number. They vary in a regular way with bond length and the electronegativity of the cation to which they are bonded, exhibiting radii close to atomic radii when bonded to a highly electronegative cation and radii close to ionic radii when bonded to a highly electropositive cation. The electron density distributions show that anions are not spherical but exhibit several different radii in different bonded directions. The bonded radii of cations correlate with ionic and atomic radii. But unlike ionic radii, the bonded radius of a cation shows a relatively small increase in value with an increase in coordination number. In contrast to atomic and ionic radii, the bonded radius of an ion in a crystal or molecule can be used as a reliable and well-defined estimate of its radius in the direction of its bonds. Received April 16, 1996 / Revised, accepted August 6, 1996     

Ab initio 2-D periodic Hartree–Fock study of Fe-substituted lizardite 1T– a simplified cronstedtite model

 A 2-D periodic ab initio Hartree–Fock LCAO study was performed on Fe-substituted 1:1 sheet silicate, lizardite. The atomic orbitals were described by large-core pseudopotentials (Fe atoms) and a sp basis set (the other atoms). Calculated atomic charges and the results of bond population analysis indicate that the Fe-O bond was as ionic as the Mg-O. This hypothesis was supported by calculated density of states and electron density maps. Increasing Fe for Mg substitution changed the shape of projected density of states (PDOS) of O(p) orbitals. Received: 27 January 2000 / Accepted: 21 May 2000     

SiO and GeO bonded interactions as inferred from the bond critical point properties of electron density distributions

The topological properties of the electron density distributions for more than 20 hydroxyacid, geometry optimized molecules with SiO and GeO bonds with 3-, 4-, 6- and 8-coordinate Si and Ge cations were calculated. Electronegativities calculated with the bond critical point (bcp) properties of the distributions indicate, for a given coordination number, that the electronegativity of Ge (∼1.85) is slightly larger than that of Si (∼1.80) with the electronegativities of both atoms increasing with decreasing bond length. With an increase in the electron density, the curvatures and the Laplacian of the electron density at the critical point of each bond increase with decreasing bond length. The covalent character of the bonds are assessed, using bond critical point properties and electronegativity values calculated from the electron density distributions. A mapping of the (3, −3) critical points of the valence shell concentrations of the oxide anions for bridging SiOSi and GeOGe dimers reveals a location and disposition of localized nonbonding electron pairs that is consistent with the bridging angles observed for silicates and germanates. The bcp properties of electron density distributions of the SiO bonds calculated for representative molecular models of the coesite structure agree with average values obtained in X-ray diffraction studies of coesite and danburite to within ∼5%. Received: 18 August 1997 / Revised, accepted: 19 February 1998     

Quantum-mechanical Hartree-Fock study of calcite (CaCO3) at variable pressure,and comparison with magnesite (MgCO3)

The static crystal energy of calcite and its structure configuration as functions of pressure were determined by ab initio all-electron periodic Hartree-Fock calculations (CRYSTAL code). Ca, O and C atoms were represented by 22, 18 and 14 atomic orbitals, respectively, in form of contracted Gaussian-type functions. Comparison between theoretical and experimental data was performed for binding energy, equilibrium unit-cell and bond lengths, bulk modulus and C ₃₃ and C ₁₁ + C ₁₂ elastic constants, and vibrational frequency of the symmetrical C-O stretching mode. The agreement is generally satisfactory. A larger compressibility is observed for structural parameters of calcite than for those of magnesite coming from a similar calculation. The Ca-O and C-O chemical bonding was characterized by electron density maps and by Mulliken atomic charges; these are discussed and compared to values determined by empirical fitting of Born-type interatomic potentials.     

Critical point properties of electron density distributions for oxide molecules containing first and second row cations

 Minimum energy geometries and electron density distributions, ϱ(r), for ∼40 polyatomic oxide molecules containing first and second row M-cations have been calculated at the Hartree-Fock level with a 6-311++G** basis set. The nature of the bonded interactions in these molecules is examined in terms of the relative electronegativities, χ _M , of the M-cations and the properties of the electron density distribution, ϱ(r _c ), evaluated at the bond critical points, r _c , along each MO bond. As ϱ(r _c ) and the Laplacian of ϱ(r _c ) increase, χ _M increases indicating an increase in the covalent character of the bonded interactions between M and O. The ratios of the curvatures of ϱ(r _c ) indicate that the NO bond is predominantly covalent, that the CO and SO bonds are of intermediate type and that the remaining MO bonds are indicated to be predominantly ionic in character. A comparison of the critical point properties of ϱ(r _c ) and χ _M indicates that the minimum energy MO bond length is an important determinate of the properties of ϱ(r _c ) and the character of the MO bonds. On the other hand, values of the local energy density, H(r _c ), indicate that the LiO, BeO, NaO, MgO and AlO bonds are predominantly ionic and that the BO, CO, NO, SiO, PO and SO bonds are predominantly covalent in character. The χ _M -values provided by the properties of ϱ(r _c ) indicate that the covalent component of a bond increases with decreasing bond length, coordination number and increasing bond strength. Each MO bond seems to represent a unique entity and to possess a distinct set of ϱ(r _c ) properties, the distinction being greater for the more electronegative cations. The bonded radius of the oxide ion, r _b (O), and the χ _M -values determined from ϱ(r _c ) correlate with values determined from promolecule electron density distributions. In addition, r _b (O) and χ _M -values determined from experimental electron density distributions for crystals correlate with values determined from procrystal electron density distributions. The number of critical points and bond paths are modeled rather faithfully by procrystal and promolecule electron density distributions, despite the neglect of the binding forces in their constructions. Received: October 15, 1996/Revised, accepted: February 10, 1997     

Experimental and theoretical bond critical point properties for model electron density distributions for earth materials

Generalized X-ray scattering factor model experimental electron density distributions and bond critical point, bcp, properties generated in recent studies for the earth materials stishovite, forsterite, fayalite and cuprite with high energy single crystal synchrotron X-ray diffraction data and those generated with high resolution diffraction data for coesite and senarmonite were found to be adequate and in relatively good agreement, ~5% on average, with those calculated with quantum chemical methods with relatively robust basis sets. High resolution low energy single crystal diffraction data, recorded for the molecular sieve AlPO₄-15, were also found to yield model electron density distribution values at the bcp points for the AlO and PO bonded interactions that are in relatively good to moderately good agreement with the theoretical values, but the Laplacian values of the distribution at the points for the two bonded interactions were found to be in relatively poor agreement. In several cases, experimental bcp properties, generated with conventional low energy X-ray diffraction data for several rock forming minerals, were found overall to be in poorer agreement with the theoretical properties. The overall agreement between theoretical bcp properties generated with computational quantum methods and experimental properties generated with synchrotron high energy radiation not only provides a basis for using computational strategies for studying and modeling structures and their electron density distributions, but it also provides a basis for improving our understanding of the crystal chemistry and bonded interactions for earth materials. Theoretical bond critical point properties generated with computational quantum methods are believed to rival the accuracy of those determined experimentally. As such the calculations provide a powerful and efficient method for evaluating electron density distributions and the bonded interactions for a wide range of earth materials.Dedicated to Professor Robert F. Stewart of Carnegie Mellon University on his retirement for his brilliant and original work modeling electron density distributions.     

A physical basis for Pauling's definition of bond strength

 The average strength, s, of the bonded interactions comprising a cation containing oxide anion coordination polyhedron and the value of the electron density, ρ(r _c ), at the bond-critical points are inversely correlated with bond length. In each case, the observed bond lengths, R, were modeled with power-law expressions defined in terms of s/r and ρ(r _c )/r, respectively, where r is the Periodic Table row number of the cation involved in the bonded interaction. On the basis of the close connection between bond strength and the value of the electron density at the bond-critical point, we conclude that bond strength is a direct measure of bond type; the greater its value, the greater the localization of electron density in the binding region and the greater the shared–electron covalent character of the bonded interaction. Received: 15 October 2002 / Accepted: 17 February 2003 Present address:G. V. Gibbs in care of M. Spackman Department of Chemistry, University of New England, Armidale 2351, Australia Acknowledgements The NSF is thanked for supporting this study with grant EAR–9627458. The paper was written while GVG was a Visiting NSF Scholar at The University of Arizona. The faculty and graduate students of the Department of Geosciences and Bob Downs and Marelina Stimpf in particular are thanked for making the visit great fun.     

Experimental multipole-refined and theoretical charge density study of LiGaSi<Subscript>2</Subscript>O<Subscript>6</Subscript> clinopyroxene at ambient conditions

The synthetic LiGaSi₂O₆ clinopyroxene is monoclinic C2/c at room-T. Its experimental electron density, ρ(r), has been derived starting from accurate room-T single-crystal diffraction data. Topological analysis confirms an intermediate ionic-covalent character for Si–O bonding, as found by previous electron-density studies on other silicates such as diopside, coesite and stishovite. The non-bridging Si–O bonds have more covalent character than the bridging ones. The Ga–O bonds have different bonding characters, the Ga–O2 bond being more covalent than the two Ga–O1 bonds. Li–O bonds are classified as pure closed-shell ionic interactions. Similar to spodumene (LiAlSi₂O₆), Li has sixfold coordination, but the bond critical points associated to the two longest bonds are characterized by very low electron density values. Similar to what previously found in spodumene and diopside, O···O interactions were detected from the topological analysis of ρ(r), and indicate a cooperative interaction among the lone pairs of neighbouring oxygen atoms. In particular, this kind of interaction has been obtained for the O1···O1 edge shared between two Ga octahedra. Integration over the atomic basins gives net charges of −1.39(10), 2.82(10), 1.91(10) and 0.82(8) e for O (averaged), Si, Ga and Li atoms, respectively. Periodic Hartree–Fock and DFT calculations confirm the results obtained by multipole refinement of the experimental data. Moreover, the theoretical topological properties of the electron density distribution on the Si₂O₆ group are very similar to those calculated for spodumene. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Bond length variation in hydronitride molecules and nitride crystals

Bond lengths calculated for the coordination polyhedra in hydronitride molecules match average values observed for XN bonds involving main group X-cations in nitride crystals to within 0.04 Å. As suggested for oxide and sulfide molecules and crystals, the forces that determine the average bond lengths recorded for coordinated polyhedra in hydronitride molecules and nitride crystals appear to be governed in large part by the atoms that comprise the polyhedra and those that induce local charge balance. The forces exerted on the coordinated polyhedra by other parts of the structure seem to play a small if not an insignificant role in governing bond length variations. Bonded radii for the nitride ion obtained from theoretical electron density maps calculated for the molecules increase linearly with bond length as observed for nitride crystals with the rock salt structure. Promolecule radii calculated for the molecules correlate with bonded and ionic radii, indicating that the electron density distributions in hydronitride molecules possess a significant atomic component, despite bond type.     

Electron density distribution and bond critical point properties for forsterite, Mg2 SiO4, determined with synchrotron single crystal X-ray diffraction data

A generalized X-ray scattering factor model experimental electron density distribution has been generated for the orthosilicate forsterite, using an essentially extinction and absorption free set of single crystal diffraction data recorded with intense, high energy synchrotron X-ray radiation (E=100.6 keV). A refinement of the model converged with an R(F)=0.0061. An evaluation of the bond critical point, bcp, properties of the distribution at the (3, –1) stationary points for the SiO and MgO bonded interactions, yielded values that agree typically within ~5%, on average, with theoretical values generated with quantum chemical computational strategies, using relatively robust basis sets. On the basis of this result, the modeling of the experimental distribution is considered to be adequate. As the bcp properties increase in magnitude, the MgO and SiO bonds decrease in length as calculated for a number of rock forming silicates. As asserted by Coppens (X-ray charge densities and chemical bonding. Oxford University Press, Oxford, 1997), large negative ²(r_c) values, characteristic of shared interactions involving first row atoms, may not be characteristic of closed shell covalent bonded interactions involving second row Si, P and S atoms bonded to O. This study adds new evidence to the overall relatively good agreement between theoretical bcp properties generated with computational quantum strategies, on the one hand, and experimental properties generated with single crystal high energy synchrotron diffraction data on the other. The similarity of results not only provides a basis for using computational strategies for studying and modeling structures, defects and the reactivity of representative structures, but it also provides a basis for improving our understanding of the crystal chemistry of earth materials and the character of the SiO bonded interaction.     

Multipole-refined charge density study of diopside at ambient conditions

The experimental multipole electron density, ρ(r), of diopside was derived from high-resolution single-crystal diffraction at room temperature. Its topological analysis revealed predominantly ionic Si–O bonding, as found in electron density studies of other silicates. In particular, the non-bridging Si–O bonds are slightly less ionic in character than the bridging Si–O bonds. The Ca–O and Mg–O bonds are classified as pure closed-shell ionic interactions. An analysis of –∇²ρ(r) showed the presence of maxima around the oxygen atoms, associated to lone pairs domains that are involved in bonds with the surrounding ions. Calculation of atomic basins gave net charges of –1.56(12), 3.11(17), 1.79(13) and 1.88(18) e for O (averaged), Si, Ca and Mg atoms, respectively. O···O interactions between the O atoms at the vertices of the SiO₄ tetrahedron were also detected from the topological analysis of ρ(r), and indicate a cooperative interaction among the lone pairs of neighbouring oxygen atoms. All these results were also confirmed by periodic restricted Hartree–Fock (RHF) calculations. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Computer simulation of electron transfer at hematite surfaces

Molecular dynamics simulations in combination with ab initio calculations were carried out to determine the rate of electron transfer at room temperature in bulk hematite (α-Fe₂O₃) and at two low-index surfaces, namely the (012) and (001) surfaces. The electron transfer reactions considered here involve the II/III valence interchange between nearest-neighbor iron atoms. Two electron transfer directions were investigated, namely the basal plane and c direction electron transfers. Electron transfer rates obtained in bulk hematite were in good agreement with ab initio electronic structure calculations thus validating the potential model. The surfaces were considered both in vacuum and in contact with an equilibrated aqueous solution. The reorganization energy is found to increase significantly at the first surface layer and this value is little affected by the presence of water. In addition, in the case of the (012) surface, the electronic coupling matrix element for the topmost basal plane transfer was calculated at the Hartree-Fock level and was found to be weak compared to the corresponding electron transfer in the bulk. Therefore, most surfaces show a decrease in the rate of electron transfer at the surface. However, where iron atoms involved in the electron transfer reaction are directly coordinated to water molecules, water lowers the free energy of activation to a great extent and provides a large driving force for electrons to diffuse toward the bulk thus opposing the intrinsic surface effect. The surfaces considered in this work show different electron transfer properties. Hematite has been shown to exhibit anisotropic conductivity and thus different surfaces will show different intra- and inter-layer rates depending on their orientation. Moreover, the calculations of electron transfers at the hydroxyl- and iron-terminated (001) surfaces revealed that surface termination has a significant effect on the electron transfer parameters in the vicinity of the surface. Finally, our findings indicate that undercoordinated terminal iron atoms could act as electron traps at the surface.     

Bond rolling resistance and its effect on yielding of bonded granulates by DEM analyses

A discrete element modelling of bonded granulates and investigation on the bond effect on their behaviour are very important to geomechanics. This paper presents a two‐dimensional (2‐D) discrete element theory for bonded granulates with bond rolling resistance and provides a numerical investigation into the effect of bond rolling resistance on the yielding of bonded granulates. The model consists of mechanical contact models and equations governing the motion of bonded particles. The key point of the theory is that the assumption in the original bond contact model previously proposed by the authors (55th CSCE‐ASCE Conference, Hamilton, Ont., Canada, 2002; 313–320; J. Eng. Mech. (ASCE) 2005; 131 (11):1209–1213) that bonded particles are in contact at discrete points, is here replaced by a more reliable assumption that bonded particles are in contact over a width. By making the idealization that the bond contact width is continuously distributed with the normal/tangential basic elements (BE) (each BE is composed of spring, dashpot, bond, slider or divider), we establish a bond rolling contact model together with bond normal/tangential contact models, and also relate the governing equations to local equilibrium. Only one physical parameter β needs to be introduced in the theory in comparison to the original bond discrete element model. The model has been implemented into a 2‐D distinct element method code, NS2D. Using the NS2D, a total of 86 1‐D, constant stress ratio, and biaxial compressions tests have been carried out on the bonded granular samples of different densities, bonding strengths and rolling resistances. The numerical results show that: (i) the new theory predicts a larger internal friction angle, a larger yielding stress, more brittle behaviour and larger final broken contact ratio than the original bond model; (ii) the yielding stress increases nonlinearly with the increasing value of β, and (iii) the first‐yield curve (initiation of bond breakage), which define a zone of none bond breakage and which shape and size are affected by the material density, is amplified by the bond rolling resistance in analogous to that predicted by the original bond model. Copyright © 2006 John Wiley & Sons, Ltd.     

Bader’s topological analysis of the electron density in the pressure-induced phase transitions/amorphization in α-quartz from the catastrophe theory viewpoint

In this work, the Bader’s topological analysis of the electron density, coupled with Thom’s catastrophe theory, was used to characterize the pressure-induced transformations in α-quartz. In particular, ab initio calculations of the α-quartz structures in the range 0–105 Gpa have been performed at the HF/DFT exchange–correlation terms level, using Hamiltonians based on a WC1LYP hybrid scheme. The electron densities calculated throughout the ab initio wave functions have been analysed by means of the Bader’s theory, seeking for some catastrophic mechanism in the sense of Thom’s theory. The analysis mainly showed that there is a typical fold catastrophe feature involving an O–O interaction at the quartz–coesite transition pressure, while the amorphization of α-quartz is coincident with an average distribution of the gradient field of the electron density around the oxygen atom which is typically observed in the free atoms. This approach is addressed to depict a phase transition from a novel viewpoint, particularly useful in predicting the stability of a compound at extreme conditions, especially in the absence of experimental data.     

Ab initio Hartree–Fock study and charge density analysis of beryl (Al4Be6Si12O36)

 An ab initio Hartree–Fock calculation on beryl structure has been performed and the wave function has been used for an analysis of the electron density. The equilibrium geometry, determined by minimizing the energy with respect to cell parameters and fractional coordinates, is in good agreement with structural experimental measurements; small differences in length between the various Si–O bonds of the structure are well reproduced by the calculation. The two non-equivalent oxygen atoms (O1 and O2) of beryl show different electron distributions. In particular, the valence shell charge concentration (VSCC) of O1 (the bridge between two Si ions) has a torus-like shape, showing a bulge on the external side of the Si–O–Si angle and a thinning on the internal side of it; by contrast O2 has two lone pairs which are approximately located on the line for O2, normal to the plane passing, on average, through the atoms O2, Si, Be and Al. The electron density of each oxygen is strongly polarized toward the Si ions and much less polarized towards the other cations. Such features of the VSCC of the oxygens can be recast in terms of the valence bond theory, to explain the observed differences in bond lengths. By calculating the potential inside the channels of the beryl structure, predictions could be made about the positions occupied by alkali cations, which are often found in natural minerals belonging to the beryl group: results agree in general with experimental findings, but foresee a shift of such cations off the central positions located on the six fold symmetry axis. Additionally, calculations of position and orientation of H₂O inside the channel, in the alkali-free beryl, locate the molecule close to the basal plane, with the H⋯H axis parallel to [001] or oriented at 40^∘ from it. Received: 12 December 2001 / Accepted: 6 April 2002