CNR-ISTM Istituto di Scienze e Tecnologie Molecolari c/o Dip. Chimica Fisica ed Elettrochimica dell'Università degli Studi di Milano Via C. Golgi, 19 20133 Milano Italy
Abstract: The total experimental electron density distributions rho(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the rho(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential Phi(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna21 of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these Ees values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.
Abstract: A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug-receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17 K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of SO and SN intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NHN hydrogen bond with an energy of about 50 kJ mol(-1). Key pharmacophoric features responsible for attractive electrostatic interactions include CHX hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions.
Abstract: An experimental study of the electron-density distribution rho(r) in an angiotensin II receptor antagonist 1 has been made on the basis of single-crystal X-ray diffraction data collected at a low temperature. The crystal structure of 1 consists of infinite ribbons in which molecules are connected by an N-H...N hydrogen bond and several interactions of the C-H...O, C-H...N, and C-H...S type. The molecular conformation, characterized by the syn orientation of a tetrazole and a pyrimidinone ring with respect to a phenyl spacer group, is stabilized by two short SO and SN intramolecular contacts between a substituted thiophene fragment and the other two heterocycles of 1. The electrostatic nature of these interactions is documented. Furthermore, the Laplacian of rho(r) in the plane defined by the sulfur, oxygen, and nitrogen atoms involved in these interactions shows their strongly directional character as the regions of charge concentration on the valence shell of the nitrogen and oxygen atoms directly face the regions of charge depletion on the valence shell of the sulfur atom. All the chemical bonds and the relevant intra- and intermolecular interactions of 1 have been quantitatively described by the topological analysis of rho(r). Simple relationships between the bond path lengths (R(b)) and the values of rho at the bond critical points (rho(bcp)) have been obtained for the 28 C-C bonds, the seven N-C bonds, and the four O-C bonds. For the first two classes of bonds the relationship is in the form of a straight line, whose parameters, for the C-C bonds, agree, within experimental uncertainty, with those previously derived in our laboratory from a 19 K X-ray diffraction study of crystals of a different compound. Maps of the molecular electrostatic potential phi(r) derived from the experimental charge density display features that are important for the drug-receptor recognition of 1.
Abstract: The electrostatic properties of crystals of α-glycine have been obtained from extensive X-ray diffraction data collected at approximately 23 K and carefully processed, including corrections for scan truncation losses, anisotropic extinction, and multiple reflection. From a multipole parameterization of the X-ray intensities we have obtained an unusually preciseand we are confident, accuratemodel of the total electron distribution in the crystal including the topological features, atom and group charges, the dipole moment for the glycine zwitterion, electrostatic potentials, electric field gradients at the nucleii of the three hydrogen atoms of the ammonium group, and intermolecular electrostatic energies within the crystal. We have also calculated the total interaction energies involving the six distinct types of intermolecular pairings and examined these energies in terms of the molecular arrangement.
Abstract: The photochemistry of isomeric 2-furyliden- and benzylidenoxindoles (2H-indol-2-ones) is examined. In solution E-Z isomerization is the only process via the excited singlet state (which fluoresces in glassy solution at 77 K and not at room temperature). In the crystalline state, the two (Z) derivatives are photostable, in accordance with the prediction based on the structural determination of the furylidene derivative, which adopts the unreactive Schmidt's gamma type arrangement. The (E) furylidene derivative (1a) gives efficiently (Phi = 0.3) the head-to-tail dimer, as indicated by the crystal structure, which is of the reactive alpha type, in full accord with the topochemical principles. In contrast, the corresponding benzylidene (1b) derivative reacts sluggishly (Phi < 0. 01) and mainly gives polymers, despite the fact that crystal structure determination shows that it likewise pertains to the alpha type and complies with the topochemical rules. The difference in reactivity is explained on the basis of (i) the twist of the phenyl ring with respect to the indole plane, and (ii) the higher overall cohesion energy and the lower interaction energy between facing molecules, as found from the charge density analysis for the crystals of 1b in comparison to those of 1a. This evidences a further stringent requirement for the occurrence of topochemical photodimerizations.
Abstract: E.s.r. and 1H-ENDOR/TRIPLE resonance experiments on ion pairs in solution formed by 4,4-dicyanobenzophenone ketyl and a few alkali-metal cations (7Li, 23Na, 39K and 133Cs) are reported. Spectral data for the electrolytically generated ketyl (tetra-n-butylammonium counterion) are also given. The 13C hyperfine interactions (carbonyl group) as a function of the counterions have been measured by e.s.r. techniques on the labelled radical. All h.f.s. data and their temperature variations are interpreted in the frame of an adequate ion-pair model and the conclusions are supported by MO calculations (McLachlan, INDO and MINDO/3).
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Notes: Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases was published from 1972 - 1989. In 1990 it continued as Journal of the Chemical Society, Faraday Transactions
Abstract: The substituent (OH, OC2H5, Cl, z.sbnd;CH=CH---CH=CH---) effects on the relative stabilities of Winstein and Möbius structures of the homotropylium cation, 1, have been investigated by the MNDO model. Electron donor substituent at C1, C3, C5, and C7 favor Möbius structures in the order C1,C7>C3,C5, whereas Winstein structures are stabilized by electron donor substituents at position C2, C4, and C6, and in the order C2,C6 > C4. Electron withdrawing substituents at C8 enhance stability of the homoaromatic structures, in the order OH>Cl. In any case, the substituent effect is found to be nearly additive. The reaction path for the three-carbon membered ring opening the eight-carbon membered ring inversion has been derived for all the compounds investigated. The equilibrium populations of Winstein Möbius structures were then obtained from the calculated probability distribution functions along the reaction path. The unsubstituted compound 1 was found to be a non-homoaromatic cation in the gas phase, as it adopts a Möbius conformation with a large C1-C7, internuclear distance.
Abstract: The conformational structure of 1,2-dimethoxyethane in the gas phase has been studied by Hartree-Fock and Møller-Plesset perturbation theory. Full geometry optimizations within C2 symmetry constraints for the aga structure and within C2h symmetry constraints for the aaa structure were performed using both 3-21G and 6-31G* basis sets. Our best energy estimate favors the aaa structure by 0.613 kcal mol−1, which reduces to 0.518 kcal mol−1 when the (unscaled) 3-21G zero-point energy contribution is included. The transition states for the conversion of the aaa structure into the aga structure and for the degenerate rearrangement of the ag+a structure into the ag−a structure have been determined.
Abstract: Semiempirical (MINDO and MNDO) and ab initio molecular orbital calculations (using 3-21G, 6-31G, and 6-31G* basis sets and including electron correlation through second-order Møller-Plesset calculations) have been applied in a study of the thermal rearrangements of the homotropylium cation (circumambulation, conformational ring inversion, and transannular hydride transfer). On the basis of our calculations and estimates, we conclude that the conformational ring inversion is the most facile process, with an activation energy of 28.7 kcal/mol, which is 2.2 kcal/mol lower than that for the transannular hydride transfer. The walk rearrangement is a symmetry-forbidden one-step reaction, which occurs with inversion at the migrating center and has an activation energy of 52.4 kcal/mol. The quantum theory of atoms in molecules has been applied to the chemical characterization of the transient species, through a topological analysis of the corresponding 6-31G* charge density functions. MINDO and MNDO estimates have been made of the influence that dimethyl substitution at the migrating carbon has on the activation energies. It is found that substitution makes the walk reaction energetically comparable to the ring inversion.
Abstract: Abstract: The structures of cyclooctatrienyl cation 1a, 1,3,5-cycloheptatriene 2a, norcaradiene 2b, cyclohexadienyl anion 3a, homocyclopentadienyl anion 3b, cyclopentadiene dianion 4a, and homocyclobutadiene dianion 4c were determined by ab initio MO theory at the RHF level with use of the split-valence 3-21 G basis set. All molecules, but 3a, prefer nonplanar structures. Homoaromaticity was found not to be important in anionic and neutral systems and has not been observed at all in cation 1. It can be concluded that Mobius aromaticity is preferred over homoaromaticity in stabilizing the investigated systems. The topological analysis of the electronic charge distribution supports this conclusion
Abstract: Applications of density matrix theory to the analysis of dynamic EPR and ENDOR spectra of organic radicals in solution are reviewed. Using some significant examples it is shown that lineshape analysis often uniquely provides direct kinetic information on reorganizing chemical systems at thermodynamic equilibrium. Temperature-dependent hyperfine coupling constants are shown to be useful for extracting information on the dynamical processes. The potency and drawbacks of dynamic EPR and ENDOR techniques are compared and discussed.
Abstract: The effect of substituents at the bridging carbon atom of 11,11-disubstituted 1,6-methano [10]annulenes is investigated by means of the topological theory of molecular structure 3-21G ab initio calculations of the potential energy hypersurface of the parent hydrocarbon, within C2v symmetry constraints, indicate three distinct stationary points, which correspond to the norcaradienic structure (1), the annulenic structure (2) and the transition state (TS) for their interconversion. Topological analysis of the charge density of the three stationary points shows that 1 is built by two 6MRs and one 3MR condensed on the C1---C6 bond, while 2 is formed by two 7MRs which share the C1---C11 and C6---C11 bonds. In TS the 3MR and C1---C6 bond critical points merge to yield a singularity in and the system goes through a catastrophe configuration of the bifurcative type. The bond equalization in 2 is far from being complete and, beside the fundamental 10Ï€-electron aromatic system, a conjugative coupling of the bridging bonds to the [10]annulenic framework is of a clear-cut relevance.
Abstract: The experimental data on a series of 11,11-disubstituted methane-[10]annulenes and 11,11-disubstituted tricyclo[4,4,1,01,6]undeca-2,4,7,9-tetraenes allow the estimation of the molecular geometry along the ring closure reaction path for the parent hydrocarbon. Ab initio calculations of the energy as a function of the reaction coordinate indicate the existence of two minima corresponding to the open and closed structures.
Abstract: A general iterative least-squares procedure for the lineshape fitting of dynamic EPR spectra in the fast motional region is outlined. The method makes use of the full information content of a spectrum, and allows the choice of different minimization algorithms in order to ensure convergence to the correct solution and speed in the least-squares fitting. Basic equations are derived, which explicitly include the effect of relatively large modulation amplitude and/or microwave power on lineshape. The algorithm adopted produces both in-phase and out-of-phase spectra, detected at any harmonic of the modulation field. These models and procedures are incorporated in the computer program EPR80, which is able to handle any problem, whose size (i.e., the number of allowed transitions and parameters) is limited only by the available main storage and the available CPU time of the computer. A few examples, relative to the EPR spectra of p-nitrobenzoate dianion radical and 2-nitro-3-aminopyridine anion radical, illustrate the application of the program.
Abstract: The mechanism of chemical and electrolytic reduction of cis- and trans-p-nitro-beta-bromostyrenes has been studied by e.s.r. spectroscopy. Both isomers undergo dehydrobromination by electrolytic reduction, whereas chemical reduction by potassium t-butoxide also induces debromination. The anion radicals of cis- and trans-p-nitro-beta-bromostyrenes, p-nitrostyrene, p-nitrophenylacetylene, and p-nitrobenzoic acid were identified, through the corresponding e.s.r. spectra, as intermediates or products of the reactions investigated. p-Nitrophenylacetylene and p-nitrobenzoic acid were also isolated from the reaction mixture. The effects of the solvent and the counterion on the yield of electrolytic conversion of cis-p-nitro-beta-bromostyrene to p-nitrophenylacetylene are also reported
Abstract: Reduction of aromatic compounds A (A = nitrobenzene,1,2-dinitrobenzene, 1,3-dinitrobenzene, 1,4-dinitrobenzene, 3-nitropyridine, 3,5-dinitropyridine, 4-nitrobenzophenone, 4,4-dinitrobenzophenone, benzonitrile, 1,2-dicyanobenzene, 1,3-dicyanobenzene, 1,4-dicyanobenzene, and 4,4-dicyanobenzophenone) by alkali metals in ethereal solvents containing sodium tetraphenylborate, yields ion pairs A–Na+, which are in equilibrium with the corresponding triple ions Na+A–Na+. In a few cases side reactions in the formation equilibria of triple ions are observed by e.s.r. spectroscopy. The decomposition of sodium tetraphenylborate is ascertained and the formation of biphenyl and p-benzosemiquinone is explained as dependent on the number and the position of the substituents in the radical anion A–
Abstract: The degree of hydration of the [gamma]-Al2O3 surface governs (a) the type of interaction between phthalocyaninato cobalt(II), [Co(pc)], and [gamma]-Al2O3; (b) the activation of [Co(pc)] towards O2 reduction; (c) the fixation of O–2 to Al3+ centres.Thermal, spectroscopic and spectromagnetic analyses show that: (a) the complex [Co(pc)] interacts with the support, as expected for a basic molecule fixed to an acidic surface; (b) O2 is reduced by the cobalt complex; (c) the initial stage of interaction between [gamma]-Al2O3[Co(pc)] and O2 is formation of the adduct [Co(pc)]O2 on the [gamma]-Al2O3 surface, followed by O–2 fixation on the Al3+ centres. Competition exists between [Co(pc)] and Al3+ as for O–2 coordination.
Notes: Journal of the Chemical Society, Faraday Transactions 1: Physical Chemistry in Condensed Phases was published from 1972 - 1989. In 1990 it continued as Journal of the Chemical Society, Faraday Transactions
Abstract: This volume records the proceedings of an international symposium on 'Advanced Magnetic Resonance Techniques in Systems of High Molecular Complexity', held in May 1985 in Siena, Italy. The meeting was attended by internationally acknowledged leaders in the various fields of magnetic resonance. The scientific discussion which followed the various lectures and presentations pointed to how magnetic resonance spectroscopies could be used to investigate physical, chemical and biological problems at all levels of complexity and molecular organization. Particular emphasis was placed on nuclear magnetic resonance dispersion. In vivo and in vitro applications of NMR techniques where discussed. EPR advances - particularly with respect to variable magnetic fields and the analysis of linewidth - were among the many other subjects treated in depth.
Abstract: PAMoC, an acronym for Properties of Atoms and Molecules in Molecular Crystals, is a complete system of programs for the analysis of any given experimental or theoretical charge density distribution.
It is simple, fast, robust, and accurate.
As distinct from other commonly used packages, the emphasis is on providing a tool to extract the biggest amount of information from a given set of experimental or theoretical results, in a way that should be easy, friendly, and exciting even to the unexperienced user.
