DFT studies of the phenol adsorption on boron nitride sheets

We perform first principles total energy calculations to investigate the atomic structures of the adsorption of phenol (C₆H₅OH) on hexagonal boron nitride (BN) sheets. Calculations are done within the density functional theory as implemented in the DMOL code. Electron-ion interactions are modeled according to the local-spin-density-approximation (LSDA) method with the Perdew-Wang parametrization. Our studies take into account the hexagonal h-BN sheets and the modified by defects d-BN sheets. The d-BN sheets are composed of one hexagon, three pentagons and three heptagons. Five different atomic structures are investigated: parallel to the sheet, perpendicular to the sheet at the B site, perpendicular to the sheet at the N site, perpendicular to the central hexagon and perpendicular to the B-N bond (bridge site). To determine the structural stability we apply the criteria of minimum energy and vibration frequency. After the structural relaxation phenol molecules adsorb on both h-BN and d-BN sheets. Results of the binding energies indicate that phenol is chemisorbed. The polarity of the system increases as a consequence of the defects presence which induces transformation from an ionic to covalent bonding. The elastic properties on the BN structure present similar behavior to those reported in the literature for graphene.     

Density functional studies of the stepwise substitution of pyridine,pyridazine, pyrimidine,pyrazine, and 1,3,5-triazine with BCO

Ozone (O₃) adsorption on pristine Stone–Wales (SW) defective BC₃ graphene-like sheets was investigated using density functional calculations. It was found that O₃ is weakly adsorbed on the pristine sheet. Two types of SW-defective sheets were studied, SW-CC and SW-BC, in which a defect is formed by rotating a C–C or B–N bond, respectively. O₃ molecules were found to be more reactive on SW-BC defective sheets. It was predicted that O₃ molecules are reduced to O₂ molecules on SW-BC sheets, overcoming an energy barrier of 34.2 kcal/mol^?1 at the B3LYP level of theory and 27.2 kcal/mol^?1 at the BP98 level of theory. Therefore, SW-BC sheets could potentially be employed as a metal-free catalyst for O₃ reduction. The HOMO–LUMO gap of a SW-BC sheet decreases from 2.16 to 1.21 eV after O₃ dissociation on its surface in the most stable state.     

Probing the effect of nitro groups in nitramine based energetic molecules: a DFT and charge density study

The structure, electron density distribution, energetic and electrostatic properties of simple nitramine based energetic TMA, DMNA, MDA and TNA molecules were determined using density functional theory (B3LYP) with the 6-311G^** and aug-cc-pVDZ basis sets coupled with Bader's theory of atoms in molecules. In the NO₂ group substituted molecules, the N–N bond distance increases with the increase of NO₂ groups, whereas in C–N bonds, this effect is relatively less, and the distances are almost equal. The topological analysis of electron density reveals that the electron density ρ_bcp(r) of C–N and N–N bonds are significantly decreasing with the increase of NO₂ groups in the nitramine molecules. The Laplacian of electron density ▽²ρ_bcp(r) of N–NO₂ bonds [DMNA: ? 16.7 eÅ^? 5, MDA: ? 12.8 eÅ^? 5 and TNA: ? 7.9 eÅ^? 5] of the molecules are relatively less negative, and the values also decrease with the increase of NO₂ groups; this implies that the charge concentration decreases with the increase of NO₂ groups, which leads to weakening the N–N bonds of the molecules. The isosurface of molecular electrostatic potential displays high electronegative regions around the NO₂ groups. The oxygen balance OB₁₀₀ of the molecules increases as the number of NO₂ group increases in the molecules, in which, the TNA molecule having maximum OB₁₀₀ value [+7.89]. The band gap, heat of detonation, bond dissociation energy and charge imbalance are predominantly depends on the number of NO₂ group present in the molecule. The charge imbalance parameter (ν) has been calculated for all molecules, which reveals that TNA is a highly sensitive molecule, the corresponding ν value is 0.047.     

The role of CS<Subscript>2</Subscript> in CS<Subscript>2</Subscript>/NMP mixed solvent in weakening the hydrogen bond of OH–N in coal: a DFT investigation

The interaction processes of trace amounts of N-methyl-2-pyrrolidinone (NMP), CS₂/NMP (1:1 by volume) and pure NMP solvent with the hydrogen bond of OH?N in coal were constructed and simulated by density functional theory methods. The distances and bond orders between the main related atoms, and the hydrogen bond energy of OH?N were calculated. The calculated results show that pure NMP solvent does not weaken the hydrogen bond of OH?N in coal. However, trace amounts of NMP and CS₂/NMP (1:1 by volume) have a strong capacity to weaken the hydrogen bond of OH?N in coal. The H2–N3 distances are elongated from 1.87 Å to 3.80 Å and 3.44 Å, the bond orders of H2–N3 all disappear, and the corresponding hydrogen bond energies of OH?N in coal decrease from 45.72 kJ mol^?1 to 7.06 and 11.24 kJ mol^?1, respectively. These results show that CS₂ added to pure NMP solvent plays an important role in releasing the original capacity of NMP to weaken the hydrogen bond of OH?N in coal, in agreement with experimental observations.     

Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5·dC5, d(TATAT):d(ATATA), and dA5·dT5 in the B and Z forms of DNA

Molecular mechanical energy refinement of double-helical pentanucleotide tetra-phosphates, d(CGCGC):d(GCGCG), dG₅·dC₅, d(TATAT):d(ATATA), and dA₅ ·dT₅ geometries, are presented in order to examine the energy required to open the Nl(purine) …? N3(pyrimidine) distance (base-pair opening) of a Watson-Crick base pair from its normal value of 3 Å to a value of 6 Å. The structural consequences of forcing base-pair opening is sequence dependent. For both dA₅ ·dT₅ and d(TATAT):d(ATATA), forcing the Nl (AdeKN3 (Thy) distance of the central base pair to a value of 6 Å slides the bases perpendicular to the helix axis forming a low-energy non-Watson-Crick base pair having an adenine amine hydrogen …? thymine carbonyl oxygen hydrogen bond. The two GC sequences behave differently from both AT sequences and differently from each other. Forcing the Nl(Gua) …? N3(Cyt) distance to 6 Å leads to unconventional structures in which hydrogen bonds are formed between the separated bases and the bases above or below them. These structures appear to be trapped in true local minima 6–10 kcal/mol higher in energy than the Watson-Crick structures. Preliminary simulations on d(CGCGC):d(GCGCG) in the Z geometry suggest the reason the Z form may be more refractory to proton exchange than the B form, consistent with experimental observations.     

Crystal Structure and Conformation of 8-(2-Hydroxyethylamino) and 8-(Pyrrolidin-1-yl) Adenosines

In the course of investigation of 8-alkylamino substituted adenosines, the title compounds were synthesized as potential partial agonists for adenosine receptors. The structure determination of these compounds was carried out with the X-ray crystallography study. Crystals of 8-(2-hydroxyethylamino)adenosine are monoclinic, space group P 2₁; a = 7.0422(2), b = 11.2635(3), c = 8.9215(2) Å, β = 92.261(1)°, V = 707.10(3) ų, Z = 2; R-factor is 0.0339. The nucleoside is characterized by the anti conformation; the ribose ring has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of N–H·O type. Crystals of 8-(pyrrolidin-1-yl)adenosine are monoclinic, space group C 2; a = 19.271(1), b = 7.3572(4), c = 11.0465(7) Å, β = 103.254(2)°, V = 1524.4(2) ų, Z = 4; R-factor is 0.0498. In this compound, there is syn conformation of the nucleoside; the ribose has the C(2′)-endo conformation and gauche–gauche form across C(4′)–C(5′) bond. The molecular structure is stabilized by intramolecular hydrogen bond of O–H·N type. For both compounds, the branching net of intermolecular hydrogen bonds occur in the crystal structures.     

Theoretical studies on the crystal structure, thermodynamic properties, detonation performance and thermal stability of cage-tetranitrotetraazabicyclooctane as a novel high energy density compound

The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet–Jacobs equations. Thermal stability of 3,5,7,10,12,14,15,16-octanitro- 3,5,7,10,12,14,15,16-octaaza-heptacyclo[7.5.1.1^2,8.0^1,11.0^2,6.0^4,13.0^6,11]hexadecane (cage-tetranitrotetraazabicyclooctane) was investigated by calculating the bond dissociation energy (BDE) at unrestricted B3LYP/6-31G (d) level. The calculated results show that the N–NO₂ bond is a trigger bond during thermolysis initiation process. The crystal structure obtained by molecular mechanics (MM) methods belongs to Pna2₁ space group, with cell parameters a?=?12.840 Å, b?=?9.129 Å, c?=?14.346 Å, Z?=?6 and ρ?=?2.292 g·cm^?3. Both the detonation velocity of 9.96 km·s^?1 and the detonation pressure of 47.47 GPa are better than those of CL-20. According to the quantitative standard of energetics and stability, as a high energy density compound (HEDC), cage-tetranitrotetraazabicyclooctane essentially satisfies this requirement.     

The influences of water solvent on the structures and stabilities of Na+–AD conformers

The influences of water solvent on the structures and stabilities of the complex ion conformers formed by the coordination of alanine dipeptide (AD) and Na⁺ have been investigated using supramolecular and polarizable continuum solvation models at the level of B3LYP/6-311++G**, respectively; 12 monohydrated and 12 dihydrated structures of Na⁺–AD complex ion were obtained after full geometrical optimization. The results showed that H₂O molecules easily bind with Na⁺ of Na⁺–AD complex ion, forming an ion-lone pair interaction with the Na–O bond length of 2.1–2.3 Å. Besides, H₂O molecules also can form hydrogen bonds O_W–H_W···O(1), O_W–H_W···O(2), N(1)–H(1)···O_W or N(2)–H(2)···O_W with O or N groups of the Na⁺–AD backbone. The most stable gaseous bidentate conformer C7AB of Na⁺–AD is still the most stable one in the solvent of water. However, the structure of the most unstable gaseous conformer α′B of Na⁺–AD collapses under the attack of H₂O molecules and changes into C7AB conformation. Computations with IEFPCM solvation model of self-consistent reaction field theory give that aqueous C5A is more stable than C7_eqB and that the stabilization energies of water solvent on monodentate conformers of Na⁺–AD complex ion (about 272–294 kJ/mol) are more than those on bidentate ones (about 243 kJ/mol).     

Theoretical study of the geometrical and electronic structures and thermochemistry of spherophanes

A set of supramolecular cage-structures—spherophanes—was studied at the density functional B3LYP level. Full geometrical structure optimisations were made with 6–31G and 6–31G(d) basis sets followed by frequency calculations, and electronic energies were evaluated at B3LYP/6–31++G(d,p). Three different symmetries were considered: C1, Ci, and Oh. It was found that the bonds between the benzene rings are very long to allow π-electron delocalisation between them. These spherophanes show portal openings of 2.596 Å in Spher1, 4.000 Å in Meth2, 3.659 Å in Oxa3, and 4.412 Å in Thia4. From the point of view of potential host–guest interaction studies, it should also be noted that the atoms nearest to the centre of the cavities are carbons bonded to X groups. These supramolecules seem to exhibit relatively large gap HOMO?LUMO: 2.89 eV(Spher1), 5.26 eV(Meth2), 5.73 eV(Oxa3), and 4.82 eV(Thia4). The calculated ΔH°_f (298.15 K) values at B3LYP/6–31G(d) are (in kcal mol^?1) 750.98, 229.78, ?10.97, and 482.49 for Spher1, Meth2, Oxa3, and Thia4, respectively. Using homodesmotic reactions, relative to Spher1, the spherophanes Meth2, Oxa3, and Thia4 are less strained by ?399.13 kcal mol^?1, ?390.40 kcal mol^?1, and ?411.38 kcal mol^?1, respectively. Their infrared and ¹³C NMR calculated spectra are reported.     

Adsorption and decomposition mechanism of hexogen (RDX) on Al(111) surface by periodic DFT calculations

The adsorption of hexogen (RDX) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×3) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and aluminum atoms induce the N?O and N?N bond breaking of the RDX. Subsequently, the dissociated oxygen atoms, NO₂ group and radical fragment of RDX oxidize the Al surface. The largest adsorption energy is ?835.7 kJ mol^–1. We also investigated the adsorption and decomposition mechanism of RDX molecule on the Al(111) surface. The activation energy for the dissociation steps of V4 configuration is as large as 353.1 kJ mol^–1, while activation energies of other configurations are much smaller, in the range of 70.5–202.9 kJ mol^–1. The N?O is even easier than the N?NO₂ bond to decompose on the Al(111) surface.     

Crystal Structure and Conformation of 5‐Fluorouridine: Conformational Preferences for 5‐Fluorinated Pyranosides

Crystals of 5‐fluorouridine (5FUrd) have unit cell dimensions a = 7.716(1), b = 5.861(2), c = 13.041(1)Å, α = γ = 90°, β = 96.70° (1), space group P2₁, Z = 2, ρ_obs = 1.56 gm/c.c and ρ_calc = 1574 gm/c.c The crystal structure was determined with diffractometric data and refined to a final reliability index of 0.042 for the observed 2205 reflections (I ≥ 3σ). The nucleoside has the anti conformation [χ = 53.1(4)°] with the furanose ring in the favorite C2′–endo conformation. The conformation across the sugar exocyclic bond is g⁺, with values of 49.1(4) and ? 69.3(4)° for Φ_θc and Φ_∞ respectively. The pseudorotational amplitude τ_m is 34.5 (2) with a phase angle of 171.6(4)°. The crystal structure is stabilized by a network of N–H…O and O–H…O involving the N3 of the uracil base and the sugar O3′ and O2′ as donors and the O2 and O4 of the uracil base and O3′ oxygen as acceptors respectively. Fluorine is neither involved in the hydrogen bonding nor in the stacking interactions. Our studies of several 5‐fluorinated nucleosides show the following preferred conformational features: 1) the most favored anti conformation for the nucleoside [χ varies from ? 20 to + 60°] 2) an inverse correlation between the glycosyl bond distance and the χ angle 3) a wide variation of conformations of the sugar ranging froni C2′–endo through C3′–endo to C4′–exo 4) the preferred g⁺ across the exocyclic C4′–C5′ bond and 5) no role for the fluorine atom in the hydrogen bonding or base stacking interactions.     

Time-dependent density functional theory study on the electronic excited-state hydrogen bonding of the chromophore coumarin 153 in a room-temperature ionic liquid

In the present work, in order to investigate the electronic excited-state intermolecular hydrogen bonding between the chromophore coumarin 153 (C153) and the room-temperature ionic liquid N,N-dimethylethanolammonium formate (DAF), both the geometric structures and the infrared spectra of the hydrogen-bonded complex C153–DAF⁺ in the excited state were studied by a time-dependent density functional theory (TDDFT) method. We theoretically demonstrated that the intermolecular hydrogen bond C₁?=?O₁···H₁–O₃ in the hydrogen-bonded C153–DAF⁺ complex is significantly strengthened in the S₁ state by monitoring the spectral shifts of the C=O group and O–H group involved in the hydrogen bond C₁?=?O₁···H₁–O₃. Moreover, the length of the hydrogen bond C₁?=?O₁···H₁–O₃ between the oxygen atom and hydrogen atom decreased from 1.693 Å to 1.633 Å upon photoexcitation. This was also confirmed by the increase in the hydrogen-bond binding energy from 69.92 kJ mol^?1 in the ground state to 90.17 kJ mol^?1 in the excited state. Thus, the excited-state hydrogen-bond strengthening of the coumarin chromophore in an ionic liquid has been demonstrated theoretically for the first time.     

DPT tautomerization of the long A∙A* Watson-Crick base pair formed by the amino and imino tautomers of adenine: combined QM and QTAIM investigation

Combining quantum-mechanical (QM) calculations with quantum theory of atoms in molecules (QTAIM) and using the methodology of sweeps of the energetic, electron-topological, geometric and polar parameters, which describe the course of the tautomerization along the intrinsic reaction coordinate (IRC), we showed for the first time that the biologically important A?A* base pair (C_s symmetry) formed by the amino and imino tautomers of adenine (A) tautomerizes via asynchronous concerted double proton transfer (DPT) through a transition state (TS), which is the A⁺?A^? zwitterion with the separated charge, with C_s symmetry. The nine key points, which can be considered as electron-topological “fingerprints” of the asynchronous concerted A?A*?A*?A tautomerization process via the DPT, were detected and completely investigated along the IRC of the A?A*?A*?A tautomerization. Based on the sweeps of the H-bond energies, it was found that intermolecular antiparallel N6Н?N6 (7.01 kcal mol^?1) and N1H?N1 (6.88 kcal mol^?1) H-bonds are significantly cooperative and mutually reinforce each other. It was shown for the first time that the A?A*?A*?A tautomerization is assisted by the third C2H?HC2 dihydrogen bond (DHB), which, in contrast to the two others N6H?N6 and N1H?N1 H-bonds, exists within the IRC range from ?2.92 to 2.92 Å. The DHB cooperatively strengthens, reaching its maximum energy 0.42 kcal mol^?1 at IRC?=??0.52 Å and minimum energy 0.25 kcal mol^?1 at IRC?=??2.92 Å, and is accompanied by strengthening of the two other aforementioned classical H-bonds. We established that the C2H?HC2 DHB completely satisfies the electron-topological criteria for H-bonding, in particular Bader’s and all eight “two-molecule” Koch and Popelier’s criteria. The positive value of the Grunenberg’s compliance constant (5.203 Å/mdyn) at the TS_A?A*?A*?A proves that the C2H?HC2 DHB is a stabilizing interaction. NBO analysis predicts transfer of charge from σ(C2–H) bonding orbital to σ*(H–C2) anti-bonding orbital; at this point, the stabilization energy E⁽²⁾ is equal to 0.19 kcal mol^?1 at the TS_A?A*?A*?A.     

Open carbon frameworks - a search for optimal geometry for hydrogen storage

Properties of a new class of hypothetical high-surface-area porous carbons (open carbon frameworks) have been discussed. The limits of hydrogen adsorption in these carbon porous structures have been analyzed in terms of competition between increasing surface accessible for adsorption and the lowering energy of adsorption. From an analysis of an analytical model and simulations of adsorption the physical limits of hydrogen adsorption have been defined: (i) higher storage capacities in slit-shaped pores can be obtained by fragmentation/truncation of graphene sheets into nano-metric elements which creates surface areas in excess of 2600 m²/g, the surface area for infinite graphene sheets; (ii) the positive influence of increasing surface area is compensated by the decreasing energy of adsorption in the carbon scaffolds of nano-metric sizes; (iii) for open carbon frameworks (OCF) built from coronene and benzene molecules with surface areas 6500 m² g^-1, we find an impressive excess adsorption of 75–110 g?H₂/kg C at 77 K, and high storage capacity of 110–150 g?H₂/kg C at 77 K and 100 bar; (iv) the new OCF, if synthesized and optimized, could lead to required hydrogen storage capacity for mobile applications.     

Influence of point defects on the electronic properties of boron nitride nanosheets

Density functional theory was utilized to study the electronic properties of boron nitride (BN) sheets, taking into account the presence of defects. The structure considered consisted of a central hexagon surrounded by alternating pentagons (three) and heptagons (three). The isocoronene cluster model with an armchair edge was used with three different chemical compositions. In the first structure, three B–B bonds were formed where one B in the dimer was part of the central hexagon. In the second structure, three N–N–N bonds were formed at the periphery of the cluster, around the central hexagon. In the third structure, three N–N bonds were formed in a similar fashion to the first model. Our results indicated that the third structure was the most stable configuration; this exhibited planar geometry, semiconductor behavior, and ionic character. To explore the effects of doping, we replaced B and N atoms with C atoms, considering different atomic positions in the central hexagon. When an N atom was replaced with a C atom, the new structure was a semiconductor, but when a B atom was replaced with a C atom, the new structure was a semimetal. At the same time, the polarity increased, inducing covalent behavior. Replacing two N atoms with two C atoms also resulted in a semiconductor, while replacing two B atoms with two C atoms yielded a semimetal; in both cases the bonding was covalent. When three B (three N) atoms of the central hexagon were replaced with three C atoms, the new structure exhibited a transition to a conductor (remained a semiconductor) with low polarity. When monovacancies (N) and divacancies (B and N) were inserted into the lattice, the system was transformed into a covalent semiconductor. Finally, the electrostatic potential surface was calculated in order to explore intermolecular properties such as the charge distribution, which showed how the reactivity of the boron nitride sheets was affected by doping and orbital hybridization.     

Preparation and structural characterization of di-μ-azido-bis[azido(2-aminopyridine)aquo]dicopper(II), [Cu(2-ampy)(N3)2(H2O)]2

Di-μ-azido-bis[azido(2-aminopyridine)aquo]dicopper(II), [Cu(2-ampy)(N₃)₂(H₂O)]₂, was synthesized and characterized by X-ray crystallography. The crystals are triclinic, space group P$\text{1}$, with a = 7.142(1), b = 7.812(1), c = 9.727(1) Å, a = 96.52(1), β = 95.52(1), γ = 113.47(1)°, and Z = 1. The structure was refined to R_F = 0.030 for 1960 observed MoKα diffractometer data. The dimeric molecule, which possesses a crystallographic inversion center, contains both terminal and μ(1)-bridging azido groups. Each copper(II) atom is further coordinated by a 2-aminopyridine ligand (via its ring N atom) and a water molecule to give a distorted square pyramid, with the metal atom raised by 0.17 Å above the N₄ basal plane [CuN (ring) = 2.001(2), CuN (azide) = 1.962(3)–2.018(2) Å] towards the apical aquo ligand [CuO = 2.371(2) Å]. Each water molecule forms an intramolecular O?HN (amine) acceptor hydrogen bond, and is linked by two OH?N (terminal azide) intermolecular donor hydrogen bonds to adjacent dimeric complexes to yield a layer structure parallel to (001). Infrared and electronic spectral data are presented and discussed.     

The phenomenon of conglomerate crystallization. XV. Spontaneous resolution in coordination compounds. XIII. The crystallization behaviour and the crystal and molecular structure of Δ(λδ)-cis-Rh(en)2(NO2)2]Cl

The title compound, I, crystallizes in the monoclinic space group P2₁ with cell constants: a = 6.599(3), b = 11.121(2), c = 8.375(1) Å and β = 106.35(2)°; V = 589.74 ų and D(calc; Z = 2) = 1.974 g cm⁻³. The compound is isomorphous and isostructural with its Co analogue. A total of 2982 data were collected over the range of 4°  20  70°; of these, 2537 (independent and with I ⩾ 3σ(I)) were used in the structural analysis. Data were corrected for absorption (μ = 16.6 cm⁻¹) and the relative transmission coefficients ranged from 1.000 to 0.9504. Refinement was carried out for both enantiomeric configurations and the crystal used was found to contain cations with Δ(λδ) absolute configuration. The final R(F) and R_w(F) residuals were, respectively 0.0220 and 0.0239 for (−−−; i.e.Δ(λδ)) and 0.0231 AND 0.0317 FOR (+++; i.e.Λ(δλ)). Thus, the former was selected as correct for our specimen.In the case of I, as well as in the Co derivative [cis-Co(en)₂(NO₂)₂]Cl (II), the conformation of one of the rings is opposite that expected for the lowest energy conformation, which in the current case should be Δ(λλ)).The RhN(NO)₂ distances are 2.020(2) and 2.010(2) Å, while the RhN(amine) distances, trans to the NO₂ ligands are 2.085(2) and 2.093(1) Å, values distinctly longer than the other two RhN distances (2.064(1) and 2.068(1) Å). The latter are the RhN distances to the terminalNH₂ ligands located trans to each other. Thus, we observe a trans effect, which is more pronounced in I than in II, and which is of comparable magnitude to that observed in the case of the trien derivative, [cis-α-Rh(trien)(NO₂)₂]Cl(III).Parallel with an increase in metalN distances in going from [cis-α-Co(trien)NO₂)₂]Cl·H₂) (IV) to (III) is an increase in the torsional angles of the outer rings (NCCN) of about 10°. Comparison of these parameters in I and II reveal that this change is not so marked for this pair since in I they are −54.9° and 52.8° while in II they are 50.2° and −48.1°; i.e. a change of only 4°. This important difference between trien and en derivatives is caused by the presence of the central five-membered ring, which for compounds III and IV remains largely unchanged, except for the metalN distances.The NO bond lengths are 1.244(3), 1.220)(2), 1.237(2) and 1.211(2) Å, which are similar to those found for the analogous Co isomer. The CN bond lengths are 1.492(3), 1.474(2), 1.486(2) and 1.475(2) Å, while the CC bonds are 1.509(3) and 1.524(3) Å. These values are also comparable with those obtained for the Co isomer and, in fact, the pattern of the bonds is nearly identical in both, including the common feature of having a longer CC bond for the en ring with the conformation opposite that expected.As was the case with the Co analogue, the Cl⁻ anion is associated with the hydrogens of the secondary nitrogen (trans to the −NO₂) ligands, the Cl…H7 distance being 2.18(3) Å and the <Cl…H7N2 = 163°.     

Synthesis and coordination chemistry of tripodal dialkyl[1,2-bis(diethylcarbamoyl)ethyl]phosphonates with lanthanide nitrates

Trifunctional dialkyl [1,2-bis(diethylcarbamoyl)- ethyl] phosphonates, (RO)₂P(O)CH[C(O)N(C₂H₅)₂]- [CH₂C(O)N(C₂H₅)₂] R  CH₃, C₂H₅, i-C₃H₇, n-C₆H₁₃ were prepared from the respective sodium salts, Na[(RO)₂P(O)CHC(O)N(C₂H₅)₂] and N,N- diethylchloroacetamide, and they were characterized by elemental analysis, mass, infrared and NMR spectroscopy. The molecular structure of (i-C₃H₇O)₂- P(O)CH[C(O)N(C₂H₅)₂][CH₂C(O)N(C₂H₅)₂] was determined by single crystal X-ray diffraction analysis and found to crystallize in the monoclinic space group P2₁/c with a=15.589(6), b=9.783(4), c= 16.283(7) Å, β = 110.90(3)°, Z = 4 and V= 2320(2) ų. The structure was solved by direct methods and blocked least-squares refinement converged with Rf = 5.7% and R_wF= 4.4% on 2266 unique data with F>4σ(F). Important bond distances include PO 1.459(3) Å, CHCO 1.228(3) Å and CHCH₂CO 1.223(3) Å. The coordination chemistry of the ligand with several lanthanides was examined, and the structure of the complex Gd(NO₃)₃{[(i-C₃H₇O)₂P(O)CH[C(O)N(C₂H₅)₂][CH₂C(O)N(C₂H₅)₂]}₂·H₂O was determined. The complex crystallized in the monoclinic space group P2₁/n with a = 13.524(5), b = 22.033(4), c = 19.604(4) Å β = 106.22(2)°, Z = 4 and V= 5609(3) ų. The structure was solved by heavy atom techniques and blocked least-squares refinement converged with R_F = 5.9% and R_wF = 4.1% on 5275 reflections with F > 4σ(F). Both trifunctional ligands were found to bond to Gd(III) through only the phosphoryl oxygen atoms. The remainder of the Gd coordination sphere was composed of three bidentate nitrate oxygen atoms and an oxygen bonded water molecule. Several important bond distances include GdO(phosphoryl)_av = 2.343(5) Å, GdO(nitrate)_av = 2.475(7) Å, GdO(water) = 2.354(5) Å, PO(phosphoryl)_av = 1.467(6) Å, CHCO_av = 1.242(10) Å and CHCH₂CO_av = 1.209(11) Å.     

Density functional and Møller–Plesset studies of cyclobutanone⋯HF and ⋯HCl complexes

The molecular structure (hydrogen bonding, bond distances and angles), dipole moment and vibrational spectroscopic data [vibrational frequencies, IR and vibrational circular dichroism (VCD)] of cyclobutanone?HX (X?=?F, Cl) complexes were calculated using density functional theory (DFT) and second order Møller–Plesset perturbation theory (MP2) with basis sets ranging from 6–311G, 6–311G^**, 6–311 + + G^**. The theoretical results are discussed mainly in terms of comparisons with available experimental data. For geometric data, good agreement between theory and experiment is obtained for the MP2 and B3LYP levels with basis sets including diffuse functions. Surface potential energy calculations were carried out with scanning HCl and HF near the oxygen atom. The nonlinear hydrogen bonds of 1.81 Å and 175° for HCl and 1.71 Å and 161° for HF were calculated. In these complexes the C=O and H–X bonds participating in the hydrogen bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and the band assignments reported are in excellent agreement with experimental IR spectra. The C=O stretching vibrational frequencies of the complexes show red shifts with respect to cyclobutanone.     

Trifurcated (Four-Center) Hydrogen Bond in Solid State Crystal Structure of 5′-Amino-5′-deoxyadenosine p-Toluenesulfonate

Abstract

The crystal structure of 5′-amino-5′-deoxyadenosine (5′-Am.dA) p-toluenesulfonate has been determined by X-ray crystallographic methods. It belongs to the orthorhombic space group P2₁2₁2₁ with a=7.754(3)Å, b=8.065(l)Å and c=32.481(2)Å. This nucleoside shows a syn conformation about the glycosyl bond and C2′-endo-C3′-exo puckering for the ribose sugar. The orientation of N5′ atom is gauche-trans about the exocyclic C4′-C5′ bond. The amino nitrogen N5′ forms a trifurcated hydrogen bond with N3, O9T and 04′ atoms. Adenine bases form A.A.A triplets through hydrogen bonding between N6, N7 and N1 atoms of symmetry related nucleoside molecules.