On heteroaromaticity of nucleobases. Bond lengths as multidimensional phenomena

Three hundred and nine carbon-carbon, carbon-nitrogen, and carbon-oxygen pi-bond lengths in high precision crystal structures of 31 purine and pyrimidine nucleobases were related to the Pauling pi-bond order, its analogues corrected to crystal packing effects, the numbers of non-hydrogen atoms around the bond, and the sum of atomic numbers of the bond atoms. Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA) demonstrated that the bond lengths in the nucleobases are three-dimensional phenomenon, characterized by nine distinct classes of bonds. Bond lengths predicted by Linear Regression models, Pauling Harmonic Potential Curves, Multiple Linear Regression, Principal Component, and Partial Least Squares Regression were compared to those calculated by molecular mechanics, semiempirical, and ab initio methods using PCA-HCA procedure on the calculated bond lengths, statistical parameters, and structural aromaticity indices. Incorporation of crystal packing effects into bond orders makes multivariate models to be competitive to semiempirical results, while further improvement of quantum chemical calculations can be achieved by geometry optimization of molecular clusters.     

Valence-bond determination of bond lengths of polycyclic aromatic hydrocarbons: comparisons with recent experimental and ab initio results

Pauling's valence-bond (VB) method for determining bond lengths is compared to ten recent literature experimental and theoretical results and is shown to give comparable results. His method only requires computation of the number of Kekulé (K) and Dewar structures (DS) of conjugated hydrocarbons. Both K and DS are obtained from the last two coefficients of the matching polynomial which is also used to obtain topological resonance energy (TRE). A molecular fragmentation method is given for determining DS of essentially disconnected polycyclic aromatic hydrocarbons (PAHs). Both Kekuléan alternant and nonalternant PAHs, including essentially disconnected and non-Kekuléan systems, have bond lengths that are easily determined by this method.     

Experimental and theoretical charge density distribution of the colossal magnetoresistive transition metal sulfide FeCr2S4

The total charge density distribution rho(r) of the colossal magnetoresistive transition metal sulfide FeCr(2)S(4) was evaluated through a multipole formalism from a set of structure factors obtained both experimentally, by means of single crystal high-quality x-ray diffraction data collected at T=23 K, and theoretically, with an extended-basis unrestricted Hartree-Fock periodic calculation on the experimental geometry. A full topological analysis, followed by the calculation of local energy density values and net atomic charges, was performed using the quantum theory of atoms in molecules. The experimental and theoretical results were compared. Good agreement was found for the topological properties of the system, as well as for the atomic net charges and the nature of the chemical bonds. An analysis of the electron density rho(r), its Laplacian nabla(2)[rho(r)], and the total energy density H(r) at the bond critical points was employed to classify all the interactions that resulted as predominantly closed shell (ionic) in nature. The topological indicators of the bonded interactions for Fe are distinct from those for Cr. The Fe-S bond distances were found to be 0.145 A shorter than the ideal values computed on the basis of Shannon's crystal radii, much shorter than the Cr-S distances with respect to their ideal Shannon lengths. Concomitantly, rho(r) and |H(r)| at the bond critical points are greater for Fe-S interactions, indicating that the local concentration of charge density in the internuclear region is larger for the tetrahedrally coordinated iron than for the octahedrally coordinated chromium. The isosurface in the real space for nabla(2)[rho(r)]=0 was plotted for both iron and chromium, pointing out the local zones of valence shell charge concentration and relating them to the partial d-orbital occupancy of the two transition metal atoms.     

Crystal structures and spectroscopic properties of zinc(II) ternary complexes of vitamin L, H' and their isomer m-aminobenzoic acid with bipyridine

The crystal structures of the three Zn(II) complexes, [Zn(bpy)(o-AB)2] (1) (bpy=2,2'-bipyridine, o-AB=o-aminobenzoic acid=Vitamin L), [Zn(bpy)(m-AB)Cl]2 (2) (m-AB=m-aminobenzoic acid), [Zn(bpy)(p-AB)Cl]*p-AB*H2O (3) (p-AB=p-aminobenzoic acid=Vitamin H'), have been determined and the basic coordination geometries and architectures organized by hydrogen-bonds and pi-pi interactions also characterized. The substitute amine group at ortho-, meta-, and para-position of AB plays an important role to produce completely different coordination motif of these complexes, further, in all complexes, aromatic amines are not coordinated to Zn(II) atom. While two different types of coordination modes of the carboxylate O atoms are present in these complexes: one mode consists of the usual Zn-O bond lengths (2.009(2)-2.251(2) A) in complex 1, 2 and 3; another consists of a very long Zn-O bond lengths (2.422(2) A) in complex 1. Each of the complexes has the characteristic UV absorption bands around 250-310 nm region, and the intense fluorescence band at near 325 nm.     

Program for predicting interatomic distances in crystals by the bond valence method

The program is a computer realization of the bond valence method (BVM), used to predict bond lengths in crystal structures from topological data. Using object-oriented programming made it possible to analyze structures of any complexity (up to 6480 crystal chemical positions). Hardware and software requirements: i486DX processor, operating system Windows 3.1/95, 4M RAM, and about 2M disk space. The program was developed at the Crystallography and Crystal Chemistry Department, Geological Faculty, Moscow State University. Translated fromZhumal Strukturnoi Khimii, Vol. 39, No. 4, pp. 708–713, July–August, 1998.     

Synthesis, structure, and redox properties of crowded triarylphosphines carrying 2,6-diarylphenyl substituents

Crowded triarylphosphines carrying 2,6-diarylphenyl and 2,4,6-trialkylphenyl groups were synthesized by the reaction of arylcopper(I) reagent with the chlorophosphines. The triarylphosphines had large bond angles and lengths around the phosphorus and were reversibly oxidized at significantly low potentials. X-ray crystallography of bis(2,4,6-triisopropylphenyl)[4-methyl-2,6-di(1-naphthyl)phenyl]phosphine revealed that two 1-naphthyl groups took anti conformation in the crystal.     

The Local Atomic Structures of Liquid CO at 3.6 GPa and Polymerized CO at 0 to 30 GPa from High‐Pressure Pair Distribution Function Analysis

The local atomic structures of liquid and polymerized CO and its decomposition products were analyzed at pressures up to 30 GPa in diamond anvil cells by X‐ray diffraction, pair distribution function (PDF) analysis, single‐crystal diffraction, and Raman spectroscopy. The structural models were obtained by density functional calculations. Analysis of the PDF of a liquid CO‐rich phase revealed that the local structure has a pronounced short‐range order. The PDFs of polymerized amorphous CO at several pressures revealed the compression of the molecular structure; covalent bond lengths did not change significantly with pressure. Experimental PDFs could be reproduced with simulations from DFT‐optimized structural models. Likely structural features of polymerized CO are thus 4‐ to 6‐membered rings (lactones, cyclic ethers, and rings decorated with carbonyl groups) and long bent chains with carbonyl groups and bridging atoms. Laser heating polymerized CO at pressures of 7 to 9 GPa and 20 GPa resulted in the formation of CO₂.     

木质素模化物键离解能的理论研究

采用密度泛函理论B3P86方法,在6-31G(d,p)基组水平上,对木质素结构中的6种连接方式(β-O-4、α-O-4、4-O-5、β-1、α-1、5-5)的63个木质素模化物的醚键(C-O)和C-C键的键离解能E_B进行了理论计算研究。分析了不同取代基对键离解能的影响以及键长与键离解能的相关性。计算结果表明,C-O键的键离解能通常比C-C键的小,在各种醚键中C_α-O键的平均键离解能最小,为182.7 kJ/mol;其次是β-O-4连接中的C_β-O键,苯环和烷烃基上的取代基对醚键的键离解能有较强的弱化作用,C-O键的键长和键离解能的相关性较差。与C-O键相比,C-C键的键离解能受苯环上取代基的影响很小,而烷烃基上的取代基对C-C键的键离解能有较大的影响,C-C键的键离解能和键长之间存在较强的线性关系,C-C键的键长越长,其键离解能越小。     

Synthesis, physical properties, multitemperature crystal structure, and 20 K synchrotron X-ray charge density of a magnetic metal organic framework structure, Mn3(C8O4H4)3(C5H11ON)2

A new magnetic metal organic framework material has been synthesized, Mn3(C8O4H4)3(C5H11ON)2, 1. Magnetic susceptibility measurements from 2 to 400 K reveal anti-ferromagnetic ordering at approximately 4 K and a total magnetic moment of 6.0 micro(B). The magnetic phase transition is confirmed by heat capacity data (2-300 K). The crystal structure is studied by conventional single-crystal X-ray diffraction data at 300, 275, 250, 225, 200, 175, 150, 125, and 100 K, and synchrotron data at 20 K. There is a phase transition between 100 and 20 K due to ordering of the diethylformamide molecules. The X-ray charge density is determined based on multipole modeling of a second 20 K single-crystal synchrotron radiation data set. The electron distributions around the two unique Mn centers are different, and both have substantial anisotropy. Orbital population analysis reveals large electron donation (1.7 e) to each Mn atom and the maximum possible number of unpaired electrons is 3.2 for both Mn sites. Thus, there is a considerable orbital component to the magnetic moment. Bader topological analysis shows an absence of Mn-Mn bonding, and the magnetic ordering is via super-exchange through the oxygen bridges. Formal electron counting suggests Mn2+ sites, but this is not supported by the Bader atomic charges, Mn1 = +0.11 e, Mn2 = +0.17 e. The topological measures show the dominant metal-ligand interactions to be electrostatic, and a simple exponential correlation is derived between Mn-O bond lengths and the values of nabla2rho at the bond critical points.     

Sterically Frustrated Aromatic Enes with Various Colors Originating from Multiple Folded and Twisted Conformations in Crystal Polymorphs**

Overcrowded ethylenes composed of 10-methyleneanthrone and two bulky aromatic rings contain a twisted carbon–carbon double (C=C) bond as well as a folded anthrone unit. As such, they are unique frustrated aromatic enes (FAEs). Various colored crystals of these FAEs, obtained in different solvents, correspond to multiple metastable conformations of the FAEs with various twist and fold angles of the C=C bond, as well as various dihedral angles of attached aryl units with respect to the C=C bond. The relationships between color and these parameters associated with conformational features around the C=C bond were elucidated in experimental and computational studies. Owing to the fact that they are separated by small energy barriers, the variously colored conformations in the FAE crystal change in response to various external stimuli, such as mechanical grinding, hydrostatic pressure and thermal heating.     

Topological electron density analysis of phosphines,phosphaalkenes and phosphaalkynes

A general survey of the topological properties of various phospines, phosphaalkenes, and phosphaalkynes is presented. Fifteen compounds containing carbon-phosphorus single, aromatic, double, and triple bonds were optimized at the Hartree-Fock-self-consistent field (HF-SCF) level using the 3-21G, 3-21G(*) and 6-31G* basis sets. Inclusion of d-orbitals was necessary to obtain reasonable structures. The electron densities of these compounds were analyzed using the topological method of Bader, revealing a number of trends. The value of the electron density at the P C bond critical point correlates strongly with the bond distance and bond order. Integrated electron populations correlate with coordination number. The integrated charge indicates a strongly polarized C P bond in all compounds. Comparisons with five C N compounds are made.     

Raman spectroscopic study of the molecular structure of the uranyl mineral zippeite from Jáchymov (Joachimsthal), Czech Republic

Raman spectra at 298 and 77K and infrared spectra of the uranyl sulfate mineral zippeite from Jáchymov (Joachimsthal), Czech Republic, K(0.6)(H(3)O)0.4[(UO(2))6(SO(4))3(OH)7].8H2O, were studied. Observed bands were tentatively attributed to the (UO(2))2+ and (SO(4))2- stretching and bending vibrations, the OH stretching vibrations of water molecules, hydroxyls and oxonium ions, and H(2)O, oxonium, and delta U-OH bending vibrations. Empirical relations were used for the calculation of U-O bond lengths in uranyl R (A)=f(nu(3) or nu(1)(UO(2))2+). Calculated U-O bond lengths are in agreement with U-O bond lengths from the single crystal structure analysis and those inferred for uranyl anion sheet topology of uranyl pentagonal dipyramidal coordination polyhedra. The number of observed bands supports the conclusion from single crystal structure analysis that at least two symmetrically distinct U6+ (in uranyls) and S6+ (in sulfates), water molecules and hydroxyls may be present in the crystal structure of the zippeite studied. Strong to very weak hydrogen bonds present in the crystal structure of zippeite studied were inferred from the IR spectra.     

Crystal structure, electronic structure, and bonding properties of anhydrous nickel oxalate

The results of crystal structure determination and theoretical analysis of electronic structure and bonding properties in relation to thermal decomposition process in anhydrous nickel oxalate are presented. The details of the methods used in this analysis i.e., the Bader’s quantum theory of atoms in molecules and bond order models (as defined by Pauling, Bader, Cioslowski and Mixon—modified by Howard and Lamarche), applied to topological properties of the electron density, obtained from ab initio calculations carried out by Wien2k FP-LAPW package (full potential linearized augmented plane wave method), as well as Brown’s bond valence model (bond valences and strengths, and bond and crystal strains, calculated from experimental crystal structure data) are described. Nickel oxalate dihydrate was prepared by precipitation from water solutions of nickel nitrate (V) with oxalic acid at about 60 °C. The crystalline powder was filtered, washed, and dried at 80 °C on air. Anhydrous nickel oxalate sample was measured by XRD method applying Philips X’Pert Pro MD diffractometer equipped with MRI high temperature cell. Structural as well as qualitative and quantitative phase analyses were made by Phillips X’Pert HighScore Plus version 2.1 software with implemented full-pattern fit by means of Rietveld method. The detailed analysis of the obtained results shows that anhydrous nickel oxalate has monoclinic crystal structure (P2₁/c, sg 14), the carbon–carbon bond is the weakest one, and the process of thermal decomposition of this structure should begin with the breaking of this particular bond followed by nickel-oxygen bonds, which will lead to metallic nickel and carbon dioxide as final products, in agreement with the experiment. These results, supported by our earlier ones show clearly that such methods (topological and structural), when used simultaneously in analysis of the crystal structure and bonding properties, provide us with the additional insight into the behavior of given compound during thermal decomposition process and thus allow predicting and explaining of its most probable pathway.     

The Bonding Structure of Quadricyclanylidene Derivatives

The crystal structures of bisquadricyclanylidene 1 , 7‐quadricyclanylidenenorbornadienes 2 and 3 are solved by X‐ray diffraction analyses. The bond lengths of the cyclopropyl moieties of 1 , 2 and 3 are compared with several other quadricyclanylidene derivatives, and the differences are analyzed by computational models. The results showed that the variation of bond lengths in this series of compounds is related to the electronic nature of substituents.     

Synthesis, structure, magnetic properties and structural distortion under high pressure of a new osmate, Sr2CuOsO6

A new osmate Sr₂CuOsO₆ was synthesized and its structure refined using powder synchrotron X-ray diffraction. The results of the Reitveld refinements indicate complete B-cation order in a double perovskite crystal structure. Furthermore, the analysis of the B-cation bond lengths indicates a symmetric coordination around Os, as opposed to a significant distortion of Cu-O bond lengths. The octahedral distortion around Cu(II) is characteristic of a Jahn-Teller distortion. Within the crystal structure of Sr₂CuOsO₆, the long Cu-O bonds are aligned in the same direction along the c-axis in the tetragonal unit cell. This parallel arrangement of long Cu-O bonds produces a lattice parameter ratio, c/(2^1/2a), that is greater than unity. The magnetic susceptibility of Sr₂CuOsO₆ was measured using a SQUID magnetometer and was observed to be consistent with an assignment of Cu(II)-Os(VI) formal oxidation states, thus confirming the bond valences calculated on the basis of the crystal structure. In perovskites, octahedral tilting and bond shortening are two competing compression mechanisms. Compression mechanisms of this double perovskite were characterized using high-pressure synchrotron X-ray diffraction. Application of hydrostatic pressure up to 6 GPa significantly decreased the lattice parameter ratio, demonstrating the primary compression mechanism is a shortening of the long Cu-O bond.     

Preparation of hexacoordinated tris(bidentate) phosphorus compounds with 1,3,2-dioxaphosphorinane rings. NMR and X-ray crystallographic studies of their conformation

A series of new unstable tris(bidentate) hexacoordinated phosphorus compounds 1 with 1,3,2-dioxaphosphorinane rings was prepared and studied by NMR and X-ray crystallography. The X-ray crystal structures showed that the 1,3,2-dioxaphosphorinane ring adopts different conformations depending on the number and size of substituents at the carbon atom C14. Substituents are deployed around the phosphorus atom in a slightly deformed octahedral structure. Deviations in bond lengths around the phosphorus atom depend on the character of the bonds and the distribution of the negative charge. (1)H and (13)C NMR measurements showed that in solution the flexibility of 1,3,2-dioxaphosphorinane ring depends on the size of substituents at the carbon C14.     

Localized Gaussian type orbital-periodic boundary condition-density functional theory study of infinite-length single-walled carbon nanotubes with various tubular diameters

The detailed geometrical structures of zigzag and armchair type single-walled carbon nanotubes (SWCNTs) with infinite tubular length were investigated using localized Gaussian type orbital-periodic boundary condition-density functional theory (LGTO-PBC-DFT) method. The structures of (n, 0) zigzag SWCNTs were optimized for n = 5-21, (n, n) armchair SWCNTs for n = 3-12. For comparison, the optimized geometry of a two-dimensional graphite sheet was also calculated. It was found that the optimized structures of the SWCNTs showed two C-C bond lengths that decrease with an increase in the tubular diameter. More specifically, the two bond lengths converged with those found in the two-dimensional graphite sheet. We also found a degeneracy in the highest occupied crystal orbitals if identical bond lengths were employed for the zigzag SWCNTs and the two-dimensional graphite sheet. This implies that the two different bond lengths found in the zigzag SWCNTs and the two-dimensional graphite sheet are probably due to the Jahn-Teller effect. The armchair SWCNTs show two slightly different bond lengths if the diameter is less than 12 A; otherwise they are almost identical, approaching the longer bond length of the two-dimensional graphite sheet. This can be due to the fact that the armchair SWCNTs do not have degeneracy in occupied crystal orbitals for identical C-C bond lengths. The crossing point of the conducting and valence bands of each armchair SWCNT were also calculated and show a diameter dependence in which the deviation from 2pi/3a decreases as diameter increases.     

Theoretical analysis of electronic and structural properties of anhydrous calcium oxalate

The results of theoretical analysis of the electronic and crystal structural properties and bonding in relation to thermal decomposition process in anhydrous calcium oxalate are presented. The methods used in this analysis—topological analysis of electron density (Bader’s Quantum Theory of Atoms in Molecules approach) obtained from DFT calculations performed by Wien2k package (Full Potential Linearized Augmented Plane Wave Method); bond order model (Cioslowski&Mixon), applied to topological properties of the electron density; as well as Brown’s Bond Valence Model (bonds valences and strength’, and bond and crystal strains, calculated from crystal structure and bonds lengths data) are described. The analysis of the obtained results shows that these methods allow us to explain the way of thermal decomposition process of anhydrous calcium oxalate to calcium carbonate as a decomposition product, and to describe the structural transition taking place during such process (from monoclinic anhydrous CaC₂O₄ to rhombohedral calcite structure). In the light of the results of our similar calculations performed previously for other anhydrous oxalates (zinc, cadmium silver, cobalt, and mercury) the proposed theoretical approach can be considered as promising and reliable tool, which allow analyzing the properties of the structure and bonding and hence predicting the most probable way of thermal decomposition process for given crystal structure.     

The substituent effect in ethylenes and acetylenes – AIM analysis

The calculations on disubstituted ethylenes YCHCHX with Y = Li, H, F and X = H, F, Li, Na, OH, BeH, NH₂, BH₂, NO₂ were performed at MP2/6-311++G(d,p) level of theory. The analysis of bond lengths and atoms in molecules based theory (AIM) topological parameters such as the characteristics of bond critical points (electron densities and their Laplacians) and atomic radii leads to the conclusion that the AIM parameters are much more sensitive to the action of intramolecular perturbations like substituents than traditional structural parameters such as bond lengths. A comparison of substituted ethylenes with the previously analyzed substituted acetylenes is also given.