Additivity of atomic static polarizabilities and dispersion coefficients

A new empirical method is proposed to evaluate the average molecular polarizabilities assuming the additivity of atomic static polarizability. Atomic static polarizability for each atom in a particular valence state is obtained. Calculated molecular polarizabilities of 94 non-halogenated compounds and of the bases in nucleic acids show the excellent agreement with experimental data.To check the further validity of this method, dispersion coefficients for CH₄, C₂H₆, C₃H₈,n–C₄H₁₀,n–C₅H₁₂,n–C₆H₁₄,n–C₇H₁₆,n–C₈H₁₈, H₂, H₂O and NH₃ are obtained from a sum of atomic terms using a London-type formula, and are compared with the accurate values of dipole oscillator strength distribution (DOSD) method. The results show the excellent agreement between theory and experiment.     

Evaluation of AM1-calculated radical cation ion-neutral complexes

AM1 semiempirical molecular orbital calculations are reported for 20 ion-neutral complexes, including hydrogen-bonded complexes, presumably involved in the gas-phase unimolecular decomposition of simple organic radical cations. The systems investigated are [C₂H₄O₂]^˙+, [C₂H₅NO]^˙+, [C₂H₆O]^˙+, [C₂H₆O₂]^˙+, [C₃H₆O]^˙+, [C₃H₆O₂]^˙+, [C₃H₈O]^˙+, and [C₃H₈O₂]^˙+. The AM1 results are compared with ab initio molecular orbital calculations at different levels of theory up to MP3/6-31G(d, p)//SCF/6-31G(d) + ZPVE and the available experimental data. AM1 fails to predict some local minima and the equilibrium geometries calculated for several complexes are found to be qualitatively different from those predicted by the ab initio calculations. However, reasonable agreement is generally found for the stabilization energies of the complexes toward dissociation into their loosely bound components. © John Wiley & Sons, Inc.     

Theoretical study on H2 elimination pathways of silylenoid H2SiLiF with CH4, NH3, H2O, HF, SiH4, PH3, H2S, and HCl

Ab initio molecular orbital calculations have been performed to explore the reaction potential energy surfaces of silylenoid H₂SiLiF with XH _n hydrides, where XH _n = CH₄, NH₃, H₂O, HF, SiH₄, PH₃, H₂S, and HCl. We have identified a previously unreported reaction pathway on each reaction surface, H₂SiLiF + H-XH _{n − 1} → H _n XSiLiF + H₂, which involves H₂ elimination following the initial formation of an association complex via a four-membered ring transition state to form the substituted three-membered ring silylenoid H _n XSiLiF and a H₂ molecule. This theoretical calculations suggest that (i) for H₂ eliminations there is a very clear trend toward lower activation barriers and more exothermic interactions on going from left to right along a given row in periodic table, and (ii) for the second-row hydrides, the H₂ elimination reactions are less exothermic than for the first-row hydrides and the reaction barriers are lower for X–S and Cl. Compared to the insertions of H₂SiLiF into XH _n , the H₂ elimination pathways should be unfavorable with higher barrier and lower exothermic.     

Uniform quality gaussian basis sets for molecular calculations. II. C2 hydrocarbons

This investigation is a continuation of a study on the optimality of MO basis sets of Gaussian functions, when constructed from AO basis sets optimized for the neutral atom or for ions. A formal charge parameter Q is used to adjust AO basis sets to the molecular environment, by virtue of a simple quadratic equation. Calculations are performed on a series of seven C₂ hydrocarbons (C₂H₂, C₂H₄, C₂H₆, C₂H₃⁺ (open), C₂H₃⁺ (bridged), C₂H₅⁺ (bridged), and C₂H₄^? radical anion). A simple rule is formulated to give approximate values of the charge parameter Q.     

Complete isomerization of the molecular ion of 1,3,5-trimethyl-2,4,6-trithian to that of 3,5,6-trimethyl-1,2,4-trithian before decomposition in the gas phase

The complete isomerization of the molecular ion of r-2-deuterio-2, cis-4,cis-6-trimethyl-1,3,5-trithian into equal proportions of 3, 5- and 6-d₁-3,5,6-trimethyl-1,2,4-trithian molecular ions adequately accounts for all major fragmentations of the former. These fragmentations are losses of C₄H₈, C₂H₄S, S₂H˙, C₄H₈S and C₂H₄S₂. Similar rearrangements are proposed for other 1,3,5-trithans and 1,3-dithians.     

Distribution of Valence Electron Density in C n H m and BnHm Framework and Polyhedral Molecules and Orbital-Reduntant Bonds

In framework molecular cations and radical cations of adamantane C₁₀H _m ^q+ and also in polyhedral molecules and molecular ions C₅H₅ ⁺, C₆H₆ ^{2 +}, B₅H₉, and B₁₀H₁₀ ^{2 -}, the charge density of valence electrons in the central areas of C _n and B _n cavities and faces is significant. In the molecule of adamantane C₁₀H₁₆, the valence electron density in central areas of the cavity and faces of the C₁₀ framework is small as compared to the electron density along its edges C-C. These distinctions are due to the fact that, in the electronic structure of C _n H ^q _m cations and radical cations and also of B _n H _m molecules and molecular ions, there is an additional orbital interaction involving vacant valence orbitals of C⁺ or B (orbital-reduntant bonds); the absence of vacant valence orbitals of C atoms in neutral adamantane molecule excludes additional orbital interactions in excess of C-H and C-C.     

Spectrophotometric Studies of the Thermodynamics of Molecular Complexation between Free Base Meso-Tetraarylporphyrins and Iodine(III) Chloride

A spectrophotometric method was used for the molecular complexation of ICl₃ with para-substituted meso-tetraarylporphyrins (H₂t(4-X)pp; X: OCH₃, CH(CH₃)₂, CH₃, H and Cl) in methanol/chloroform (2.5% v/v) solution. The equilibrium constants and the thermodynamic parameters were measured spectrophotometrically at various temperatures for 1:1 molecular complex formation of meso-tetraarylporphyrins as electron donors with ICl₃ as the electron acceptor. The formation constants for the molecular complexes change according to the following trend: [ICl₃(H₂t(4-OCH₃)pp)]>[ICl₃(H₂t(4-CH(CH₃)₂)pp)]>[ICl₃(H₂t(4-CH₃)pp)]>[ICl₃(H₂tpp)]>([ICl₃(H₂t(4-Cl)pp)]. Further, the thermodynamic parameters, ΔG ^o,ΔH ^o and ΔS ^o, for formation of the complexes were obtained.     

Similarities and differences between bis[2‐(bromomethyl)phenyl] diselenide,bis[2‐(chloromethyl)phenyl] diselenide and bis[2‐(hydroxymethyl)phenyl] diselenide

The title compounds, C₁₄H₁₂Br₂Se₂, (I), C₁₄H₁₂Cl₂Se₂, (II), and C₁₄H₁₄O₂Se₂, (III), feature a diselenide bridge between two o‐benzyl bromide [in (I)], two o‐benzyl chloride [in (II)] or two o‐benzyl alcohol units [in (III)]. In the molecular structure of (I) and in both independent molecules of (II), close contacts are observed between the halogen centres and the diselenide unit. In the case of modification (IIIa), strong hydrogen bonds between the –OH groups dominate, whereas the molecular structures of modification (IIIb) and bis{2‐[(dimethylamino)methyl]phenyl} diselenide, C₁₈H₂₄N₂Se₂, (IV), are comparable with those of (I) and (II). A correlation between the strength of the contacts and the angle between the benzene planes and the Se—Se units is found.     

Second-order quantum similarity measures from intracule and extracule densities

The calculation of quantum similarity measures from second-order density functions contracted to intracule and extracule densities obtained at the Hartree-Fock level is presented and applied to a series of atoms, (He, Li, Be, and Ne), isoelectronic molecules (C₂H₂, HCN, CNH, CO, and N₂), and model hydrogen-transfer processes (H₂/H⁺, H₂/Hot, H₂/H⁻). Second-order quantum similarity measures and indices are found to be suitable measures for quantitatively analyzing electron-pair density reorganizations in atoms, molecules, and chemical processes. For the molecular series, a comparative analysis between the topology of pairwise similarity functions as computed from one-electron, intracule, and extracule densities is carried out and the assignment of each particular local similarity maximum to a molecular alignment discussed. In the comparative study of the three hydrogen-transfer reactions considered, second-order quantum similarity indices are found to be more sensitive than first-order indices for analyzing the electron-density reorganization between the reactant complex and the transition state, thus providing additional insights for a better understanding of the mechanistic aspects of each process. Received: 7 July 1997 / Accepted: 29 October 1997     

Evaluated and estimated kinetic data for phase reactions of the hydroperoxyl radical

Methods are discussed for the production and detection of the hydroperoxyl radical for use in gas phase kinetic studies. Rate constants for gas phase reactions of the hydroperoxyl radical with itself, H₂, H₂O, CO, NO, SO₂, O₃, C₂H₆, C₃H₈, i-and n-C₄H₁₀, C₂H₄, i-C₄H₈, HCHO, C₂H₅CHO, n-C₃H₇CHO, Br, O, OH, and H are critically evaluated. Recommended or estimated rate constant expressions with associated error limits are given applicable over specified temperature ranges (normally 300–1000°K). The reactivity of HO₂ compared with OH, O, H, F, Cl, Br, CH₃, and CH₃O is presented in tabular form and the implications for atmospheric chemistry are discussed.     

Perturbative calculation of intermolecular interactions in orthogonalized or biorthogonal basis sets

Two versions of a many-body perturbation theory for the computation of molecular interaction energies are investigated. The methods are based on the partitioning of the second-quantized form of the dimer Hamiltonian written either in the orthogonalized basis of the monomer MOs, or, alternatively, in the original non-orthogonal dimer basis set handling the overlap by the biorthogonal formalism. The zeroth-order Hamiltonian H ⁰ is the sum of effective monomer Fockians and the zeroth-order wave functions are exact eigenfunctions of H ⁰. Full antisymmetry is ensured by the second-quantized formalism. Basis set superposition error is accounted for by the counterpoise correction recipe. Results for He₂, (H₂)₂ and (H₂O)₂ indicate the reliability of the biorthogonal technique.     

Redetermination of 6‐amino‐5‐formyl‐1,3‐dimethyluracil monohydrate at 120 K: a polarized molecular structure and two interwoven hydrogen‐bonded frameworks

The title compound [systematic name: 6‐amino‐5‐formyl‐1,3‐dimethylpyrimidine‐2,4(1H,3H)‐dione monohydrate], C₇H₉N₃O₃·H₂O, has been reexamined at 120 K. The improved precision of the intramolecular dimensions provides evidence for a polarized molecular–electronic structure, and the molecular components are linked by one N—H...O and two O—H...O hydrogen bonds into two interwoven three‐dimensional frameworks, which are weakly linked by the longer component of a three‐centre N—H...(O)₂ hydrogen bond.     

Bivalent metal complexes ofp-methyl- andp-methoxybenzoylhydrazone oximes

Summary Bivalent metal complexes ofp-chloro-,p-methyl- andp-methoxybenzoylhydrazone oximes (H₂BMCB, H₂BMMB or H₂BMTB=H₂L), [M(H₂L)Cl₂]. nH₂O (M=Zn^II, Cd^II or Hg^II, n=0 or 1; [M(H₂L)Cl₂] (M=Zn^II or Cd^II); [M(HL)₂(H₂O)_n]. YH₂O (M=Co^II, Cu^II, Zn^II or U^VIO₂, n=0–2); [Ni(H₂BMCB)(H₂O)₃]Cl₂, [Ni(BMMB)(H₂O)]₂ and [Ni(BMTB)(H₂O)]₂, were synthesized by conventional physical and chemical measurements. I.r. spectra show that the ligands are bidentate or tridentate. Spectral, magnetic and molecular weight measurements suggest that cobalt(II) and nickel(II) have monomeric octahedral geometry when derived from H₂BMCB, a dimeric square planar geometry for nickel(II) and monomeric square planar geometry for cobalt(II) for those isolated from H₂BMMB or H₂BMTB. Also, a monomeric distorted octahedral structure is proposed for copper(II) complexes derived from the ligands under investigation.     

Novel one-dimensional polymeric Cu(II) complexes via Cu(II)-assisted hydrolysis of the 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine pincer ligand: Synthesis,structure, and antimicrobial activities

Two unexpected one-dimensional coordination polymers, [Cu(PT)(H₂O)Cl]_n 1 and [Cu₂(BPT)(ClO₄)₃(H₂O)₄]_n·2nH₂O 2 , of symmetrical triazine-based ligands were synthesized by Cu(II)-mediated hydrolysis of the 2,4-bis(3,5-dimethyl-1H-pyrazol-1-yl)-6-methoxy-1,3,5-triazine ( MBPT ) pincer ligand. The reaction of Cu(ClO₄)₂·6H₂O with MBPT proceeded via hydrolysis of the methoxy group to produce the dicompartmental 4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazin-2(1H)-one ligand ( HBPT ) that then undergoes in situ complexation with Cu(II) to afford 2 . In case of CuCl₂, the reaction proceeds further with C–N cleavage of one pyrazolyl unit leading to the formation of 6-(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazine-2,4(1H,3H)-dione ligand ( HPT ) that also undergoes in situ complexation with Cu(II) affording 1 . The role of Cu(II) is to increase the Lewis acid reactivity of the water molecule where similar hydrolytic reactions for MBPT were observed in acidic medium in presence of an aqueous HCl (1:1 v/v) solution. The molecular and supramolecular structures of complexes 1 and 2 were investigated using X-ray diffraction of single crystal, Hirshfeld analysis, and density functional theory calculations. The Cl…H (11.7%) and O…H (24.7%) contacts are the most important in 1 , whereas the molecular packing of 2 is controlled mainly by the O…H (58.7%) hydrogen bonds. Complex 2 showed better activity against Escherichia coli, Bacillus subtilis, and Candida albicans compared with the standard antibiotics amoxicillin, tetracycline, and ampicillin. In general, complexes 1 and 2 showed good antimicrobial activity than these antibiotics and have the advantage to be used as both antibacterial and antifungal agents.     

2‐{[Bis(2‐pyridylmethyl)amino]­methyl}‐6‐[(2‐hydroxy­anilino)­methyl]‐4‐methyl­phenol: a novel binucleating asymmetric ligand as a precursor to synthetic models for metalloenzymes

The title compound (H₂L), C₂₇H₂₈N₄O₂, is an asymmetric binucleating ligand with well defined soft (N₃O‐donor) and hard (NO₂‐donor) sides. H₂L was designed as a ligand for the preparation of heterodinuclear mixed‐valence M^III/M′^II complexes which are models for heterobimetallic active sites of enzymes, principally calcineurin. The mol­ecular structure of H₂L shows a spatial pre‐organization of the donor groups for coordination. This conformation is stabilized by bifurcated intra‐ and inter­molecular O—H⋯N hydrogen bonds involving both phenol groups. The inter­molecular hydrogen bonds link mol­ecules of H₂L into chains running parallel to the crystallographic c axis.     

Refractive index and derived molecular properties of some gases determined by dispersive fourier transform spectroscopy (DFTS) in the visible wave number range

Dispersive Fourier transform spectroscopy (DFTS) is used to determine the dispersion of the real refractive indexn() of the gases CH₄, C₂H₄, C₂H₆, C₃H₈ and cyclo-C₃H₆ in the visible wave number range. Some molecular properties, e.g. oscillator strength sums, are derived from these measurements and compared with available data of literature.     

Full stereochemical understanding in a new (2R,3R,4R)-4-hydroxyisoleucine synthesis

We present the crystal and molecular structures of 2,3,6,7,8,8a-hexa­hydro-6,8-methano-7,7,8a-tri­methyl-3-(1-methyl-2-oxo­propyl­idene)-5H-1,4-benzoxazin-2-one, C₁₆H₂₁NO₃, (III), and 2,3,6,7,8,8a-hexa­hydro-3-(2-hydroxy-1-methyl­propyl)-6,8-methano-7,7,8a-tri­methyl-5H-1,4-benzoxazin-2-one, C₁₆H₂₅NO₃, (V). These compounds are two of the four key intermediates in our synthetic route to (2R,3R,4R)-4-hydroxy­isoleucine. The two structures provide a full understanding of the stereochemistry in successive steps. This synthesis was based on a new optically pure chiral oxazinone auxiliary derived from (1R,2R,5R)-2-hydroxy­pinan-3-one.     

Synthesis,Crystal Structure,and Thermal Properties of the Energetic Coordination Compound [Co(DAT)2(H2O)4](HTNR)2·2H2O (DAT = 1,5‐diaminotetrazole)

A new coordination complex, [Co(DAT)₂(H₂O)₄](HTNR)₂ · 2H₂O [DAT = 1,5‐diaminotetrazole, HTNR = 2,4,6‐trinitroresorcinol (styphnic acid)], was obtained in high yield and characterized by elemental analysis and Fourier‐transform infrared (FT‐IR) spectroscopy. The molecular structure of [Co(DAT)₂(H₂O)₄](HTNR)₂ · 2H₂O in the crystalline state is determined by X‐ray crystallography is as follows: monoclinic, C2/c, a = 19.216(3) Å, b = 5.4992(8) Å, c = 30.418(5) Å, β = 104.500(5), V = 3112.0(8) ų, Z = 4, ρ_calc. = 1.851 g · cm^–3, R₁ = 0.0271 and wR₂ = (all data) 0.0674. The central cobalt(II) cation is coordinated by two nitrogen atoms of two DAT and four oxygen atoms of four H₂O ligand molecules to form a six‐coordinate and slightly distorted octahedral structure. Extensive intermolecular hydrogen bonds link molecular units of [Co(DAT)₂(H₂O)₄(HTNR)₂ · 2H₂O together to form a 3D net structure with pore canals. The thermal decomposition mechanism for the title compound was predicted based on DSC, TG‐DTG, and FT‐IR analyses and non‐kinetic parameters of the first exothermic process were estimated by applying the Kissinger, Starink, and Ozawa–Doyle methods.     

Translational energy release and stereochemistry of steroids. VII—the loss of angular methyl groups after the dehydration of molecular ions of cholesterol and related C(5)-unsaturated 3β-hydroxy steroids

The translational energy, T, released during the loss of the angular 18- and 19-methyl groups both from metastable molecular ions and metastable [M ? H₂O]⁺ and [M ? 2H₂O]⁺ ions, in C(5)-unsaturated mono-and di-hydroxy steroids, as well as in their 19-nor and deuterated analogues bearing the label in the 19-methyl group, has been measured. It was found that, while the T values for the 19-CH₃ loss, following the dehydration of the molecular ions, are increased substantially when compared to those for the same loss from the molecular ions, the T values for the 18-CH₃ loss are increased much more moderately. Nevertheless, the amounts of translational energy released in the [M ? H₂O]⁺˙ ? 18-CH₃˙ and [M ? 2 H₂O]⁺˙ ? 18-CH₃˙ transitions are still higher than those found for the respective 19-methyl loss, in accordance with the general rule established recently.     

Three (E)‐2‐[(bromo­phen­yl)imino­meth­yl]‐4‐methoxy­phenols

The title compounds, (E)‐2‐[(2‐bromo­phenyl)imino­methyl]‐4‐methoxy­phenol, C₁₄H₁₂BrNO₂, (I), (E)‐2‐[(3‐bromo­phenyl)­imino­methyl]‐4‐methoxy­phenol, C₁₄H₁₂BrNO₂, (II), and (E)‐2‐[(4‐bromo­phenyl)imino­methyl]‐4‐methoxy­phenol, C₁₄H₁₂BrNO₂, (III), adopt the phenol–imine tautomeric form. In all three structures, there are strong intra­molecular O—H⋯N hydrogen bonds. Compound (I) has strong inter­molecular hydrogen bonds, while compound (III) has weak inter­molecular hydrogen bonds. In addition to these inter­molecular inter­actions, C—H⋯π inter­actions in (I) and (III), and π–π inter­actions in (I), play roles in the crystal packing. The dihedral angles between the aromatic rings are 15.34 (12), 6.1 (3) and 39.2 (14)° for (I), (II) and (III), respectively.