Atom Lone Pair Research Articles

Chlorine dioxide reaction with selected amino acids in water

Chlorine dioxide is a hypochlorite alternative disinfectant agent. In this context, we have determined the products formed in the reaction of ClO 2 with selected amino acids as model compounds that can be present in natural waters. The reaction of tryptophane, histidine and tyrosine (10 ppm each) with ClO 2 were studied at molar ratios ranging from 0.25 to 4 in the presence or absence of oxygen. It was found that in the absence of oxygen adding substoichiometric amounts of ClO 2 creates products that are structurally similar to the starting amino acids. Through a series of cascade reactions the initial product distribution gradually evolves toward simple, small carbon chain products that are far from the starting amino acid. The reaction product distribution revealed that chlorine dioxide can attack the electron-rich aromatic moieties as well as the nitrogen atom lone electron pair. Our study is relevant to gain knowledge on the reaction mechanism of ClO 2 with ubiquitous amino acids present in natural waters.

Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis

Hydration effects on the C[Triple Bond]N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom's lone pair orbital and with nitrile pi orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions.

Local molecular orbitals and hyper-susceptibility of TeO2 glass

The dielectric properties of the glassy telluria have been modeled and studied via the ab initio calculations of the linear- and hyper-polarizabilities of chain-like (TeO2)n clusters. By using the localized molecular orbitals approximation (GAMESS program), it is shown that their linear polarizability is mainly associated with the tellurium atom lone pairs and with the Te–O–Te bridges, whose contributions are comparable. On contrary, the bridge contributions unequivocally dominate the hyperpolarizability value (providing 75% of this) whereas the role of the lone pair on tellurium atoms is minimal (5%). The same estimations can be obtained for the relevant characteristics of TeO2 glass.

Comparison of three effective Hamiltonian models of increasing complexity: Triazene in water as a test case

A critical comparison of widely used solvation models is reported. It is illustrated by a study of the triazene molecule in liquid water. We consider the following approaches: (1) a continuum model based on multicentric multipole expansions of the charge distribution, (2) the averaged solvent electrostatic potential from molecular dynamics (ASEP/MD) method, and (3) molecular dynamics simulations using a combined quantum mechanics/molecular mechanics potential (QM/MM/MD). We find that the solvation induces appreciable changes in the geometry and charge distribution of triazene. These changes are only qualitatively reproduced by the dielectric continuum model, which clearly underestimates induced dipole moments and solute-solvent interaction energy. We also show that the use of effective point charges placed on solute nuclei during the classical simulations may cause significant errors in the description of the solvent structure. The addition of charges representing nitrogen atom lone pairs is compulsory to reproduce the QM/MM/MD simulation results. Moreover, our results validate the use of the mean field approximation in the study of solvent effects. A major conclusion of this study is that the ASEP/MD method constitutes a reliable alternative to the much more computationally demanding QM/MM/MD methods.

Geometry of Simple Molecules. 2. Modeling the Geometry of AX3E and AX2E2Molecules through the Nonbonded Interaction (NBI) Model

A new conceptual model of molecular geometry is presented, called the nonbonded interaction (NBI) model. This model is applied to the geometries of the AX3E and AX2E2 (A = N, O, P, S, As, Se, or Te; X = H, F, Cl, Br, I, CH(3), tBu, CF3, SiH3, Sn(tBu)3, or SnPh3) molecule types. For these molecules, the NBI model can be quantified on the basis of a balance between terminal atom-terminal atom (X-X) interactions and lone pair-terminal atom (E-X) interactions. The empirically observed X-A-X angles range from 91.0 degrees (SeH2) to 180 degrees (O(Sn(tBu)3)2), and the NBI model predicts the X-A-X angle with a mean unsigned error of 1.0 degrees using the empirical A-X distance, 1.5 degrees using the LMP2/6-31G** A-X distance, and 1.1 degrees using the MMFF94 A-X distance. This level of precision compares well to the LMP2/6-31G**-predicted X-A-X angles and is significantly better than the MMFF94-predicted X-A-X angles. Terminal groups that are not sufficiently spherical (CF3, SiH3, and SnPh3) can still be addressed qualitatively by the NBI model, as can molecules with a mixture of terminal groups. The NBI model is able to explain, often quantitatively, the geometry of all of the molecules studied, without any additional postulates or extensive parametrization.

The Role of Intramolecular Hydrogen Bonds vs. Other Weak Interactions on the Conformation of Hyponitrous Acid and Its Mono- and Dithio-Derivatives

High level ab initio and density functional theory calculations have been carried out to investigate the relative stability of the different conformers of hyponitrous acid and its mono- and dithio-derivatives. Geometries and vibrational frequencies were obtained at the B3LYP/6-311+G(d,p) level and final energies through B3LYP/6-311++G(3df,2pd) single point calculations. The reliability of this theoretical scheme has been assessed by comparing these DFT results with those obtained at the G3 level of theory, for some suitable cases. The cis conformers of hyponitrous acid and its mono- and dithio-derivatives are systematically more stable than the trans ones because in the cis conformation a dative interaction between the nitrogen-lone pairs and the σNX^* antibonding orbital is significantly favored. Quite interestingly, in general, the conformers presenting an intramolecular hydrogen bond (IHB) are not the global minima of the corresponding potential energy surfaces and only for hyponitrous acid the conformer with a OH ⋅s O IHB is slightly more stable than the cis conformer without IHB. The low stability of the tautomers with IHB is closely related with another weak intramolecular interaction which involves the lone-pairs of the chalcogen atoms and the πNN* antibondig orbital, and which is significantly perturbed when the IHB is formed.

Tautomerism of 9-acridinamines substituted at the exocyclic nitrogen atom in view of computational predictions and experimental findings

Abstract Ab initio and density functional methods were used to study the tautomerisation ability of 9-acridinamine and 14 of its derivatives substituted at the exocyclic nitrogen atom and to predict their structures as well as their thermodynamic and physicochemical characteristics. The structures predicted compare quite well with those available by X-ray techniques. Electronegative substituents at the exocyclic nitrogen atom favor the formation of imino tautomers. Hence, the logarithm of the equilibrium constant of the amino → imino tautomerisation increases when the resultant negative charge of the substituent at the exocyclic nitrogen atom does so. The same tendency is noted when the medium (CH3CN, H2O) is included in the calculations. Compounds containing CH3, SiH3, NH2, PH2, OH and SH substituents can exist in a previously unconsidered imino form which we have named the “imino nitrogen atom lone pair coordinating form”. This form seems to be the most stable one when SH is the substituent. The electrostatic potential around the tautomers exhibits a dipole- or quadrupole-type distribution. Analysis of this feature reveals seven patterns of electrostatic potential distribution, which take all the possible tautomers of each compound investigated into account. The importance of the results accumulated in the design of 9-acridinamines with cognitively and practically interesting properties is indicated.

Neutral and ionic multiple hydrogen bonded moieties in crystal structure of a one tripodal Schiff base

Structural and spectroscopic properties of solid tris(3-formyl-5-methyl-2-salicylidenamino-ethyl)amine have been investigated. This is a compound containing two moieties with triple Schiff base fragments. One of the moieties has all three neutral intramolecular O–H⋯N hydrogen bonds, whereas there are only ionic H-bonds in the other moiety. Both moieties form cavities with the amine N atom lone electron pairs inside strongly shielded by three aliphatic wings. The H-bond formed in the Schiff fragments influence the other structural parameters of the nearest aromatic parts of the moieties. 13C and 15N CP/MAS NMR results (chemical shifts) allow to identify two pairs of Schiff and amino nitrogen nuclei thus supporting formation of the two types of moieties in the crystal lattice.

Dimorphism in mercury(II) tellurite(IV) tellurate(VI): preparation and crystal structures of α- and β-Hg2Te2O7

Abstract The mixed-valent mercury(II) tellurite(IV) tellurate(VI), Hg2Te2O7, is dimorphous and crystallizes in two modifications with slightly different density, named α-(high density) and β-(low density). Colourless single crystals of both modifications were prepared simultaneously by chemical transport reactions, starting from stoichiometric mixtures of HgO, TeO2 and TeO3 in sealed and evacuated silica glass ampoules. A temperature gradient of 600 → 550°C was applied and small amounts of HgCl2 served as transport agent. The crystal structures (α-Hg2Te2O7: C2/c, Z = 8, a = 12.910(4), b = 7.407(2), c = 13.256(4) Å, β = 112.044(5)°, 1711 structure factors, 73 parameters, R[F 2 > 2σ(F 2)] = 0.0325, wR(F 2 all) = 0.0796; β-Hg2Te2O7: Aea2, Z = 16, a = 7.4405(12), b = 23.713(4), c = 13.522(2) Å, 3528 structure factors, 132 parameters, R[F 2 > 2σ(F 2)] = 0.0430, wR(F 2 all) = 0.0738) are not directly correlated by a supergroup-subgroup relation but show similar building units which are also found in the structure of the mixed-valent Te(IV,VI) compound BaCuTe2O7. Characteristic structural feature of both polymorphs is a slightly distorted hexagonal array made up of isolated 1 ∞[TeVIO4/1O2/2] chains running parallel to [010] for the α- and to [100] for the β-modification. The chains are interconnected via [TeIVO4] polyhedra to form infinite Te2O7 4- layers with a different topology for both structures. In α-Hg2Te2O7 the layers are linearly ordered and spread parallel to (101̅) whereas in β-Hg2Te2O7 the zig-zag arranged layers extend parallel to (001). The lone-pairs of the TeIV atoms are stereochemically active and protrude into the cavities of the structure. For both structure types the mercury atoms are situated in-between the anionic sheets and interconnect the layers into the three-dimensional network. The coordination numbers of the mercury atoms range from 6–8 in both modifications with the typical Hg–O distances between 2.03–3.0 Å.

Investigations on the Interaction Between sp 2 -Sulfur Atoms and Iodine Molecules Using the Cambridge Structural Database

The interaction between sp 2 -sulfur and iodine was investigated using the Cambridge structural database (CSD). A CSD search for fragments containing at least two iodine atoms bonded to each other and exhibiting an S·;·;·;I distance less than 5.0 Å to sp 2 -sulfur atoms yields 136 fragments. The distribution of the number of fragments over the S·;·;·;I distances shows that there are two different groups. The first group contains only fragments with S·;·;·;I distances between 2.4 and 3.1 Å and the second group between 3.5 and 5.0 Å. The analysis of the orientation of the iodine atoms and the sulfur atoms shows that in the structures of the first group the iodine atoms are oriented predominantly in the direction of the lone-pairs of the sulfur atoms, whereas for S·;·;·;I distances larger than 3.5 Å a random distribution is found. This preferred orientation can be regarded as a donor acceptor interaction which also is shown by the distribution of the S·;·;·;I-I angles. For the group with S·;·;·;I distances between 2.4 and 3.1 Å S·;·;·;I-I angles of about 180°; are found, whereas for S·;·;·;I distances larger than 3.5 Å a random distribution of these angles occurs. In agreement with these results a correlation between the intermolecular S·;·;·;I and the intramolecular I-I distances is found in the group of structures with shorter S·;·;·;I bond lengths. These results are discussed as a model for the hypothetical reaction between thioketones and iodine under formation of a cationic species.

Oxidation of the octa-(ethyl)diphosphaferrocene

The octa-(ethyl)-diphosphaferrocene ( 1) reacts with NOBF 4 in dichloromethane to yield a polymer ( 2) featuring diphosphaferrocene ligands ( 1) that bridge [Fe(NO) 2] units through their two phosphorus atom lone pairs. The X-ray crystal structure of 2 has been recorded. The formation of the 1-P-fluoro-2,3,4,5-tetra-(ethyl)-phosphole oxide as a by-product demonstrates that phosphaferrocenium ( 2) is sensitive towards substitution reaction at iron and nucleophilic attack at phosphorus. Oxidation of 1 with iodine in dichloromethane yielded the corresponding phosphaferrocenium cation [FeI 4] − complex ( 4) which has been characterized structurally. The formation of 4 probably results from the partial decomposition of the diphosphaferrocenium cation having [I 3] − as the counter anion.

Two-Dimensional Penning Ionization Electron Spectroscopy of Dichlorobenzenes: Orbital Reactivity and Anisotropic Interaction of Dichlorobenzenes with He*(23S)

Ionization of dichlorobenzenes with metastable He*(23S) atoms was studied by two-dimensional (collision-energy/electron-energy-resolved) Penning ionization electron spectroscopy. Collision energy dependence of the partial ionization cross sections (CEDPICS), which reflects the interaction potential energy between the molecule and He*(23S), showed anisotropic interaction around the molecules. The π and n (nonbonding) orbitals regions of the molecules showed attractive interactions. It was also found that the magnitude of attractive interaction around the Cl atom lone pair region perpendicular to the phenyl ring was o- > p- > m-C6H4Cl2. Negative slopes of CEDPICS for σ type bands indicate an attractive effect for ionization reaction by a substitution of the Cl atom.

Boron−Nitrogen (BN) Substitution Patterns in C/BN Hybrid Fullerenes: C60-2x(BN)x (x = 1−7)

Semiempirical AM1 and MNDO and density functional theory (B3LYP/3-21G and 6-31G*) are used to examine the relative stability of various isomers of successive BN substituted fullerenes C60-2x(BN)x, where x=1−7. It is found that stability is enhanced by keeping BN units and BN filled hexagons adjacent to one another. Successive BN substitution prefers N site attachment to the existing BN chain. The localization of MOs shows that lone-pairs of nitrogen atoms reside “inside” the cage, which may be the reason for outward displacement of N atoms. Geometric parameters and charge distribution of the carbon region of hybrid fullerenes are not much perturbed by BN substitution. Band gap (HOMO−LUMO gap), ionization potential, and electron affinities strongly depend on the number of BN units and filling of the hexagons. Partially BN filled hexagons or unsaturated BN fullerenes have a stronger effect than completely filled hexagons on perturbing these properties.

An experimental and theoretical investigation of the valence shell photoelectron spectrum of cyanogen chloride

The valence shell photoelectron spectrum of cyanogen chloride has been studied using HeI and synchrotron radiation. In the outer valence region the molecular orbital model of ionization holds, and the main bands can be associated with single-hole states. However, in the inner valence region electron correlation effects become important, and these result in complex satellite structure being observed. Vertical ionization energies and spectral intensities have been computed using the Green's function approach, and the results have facilitated an interpretation of the experimental spectra. Photoelectron angular distributions and branching ratios have been measured and have been used to assess the bonding characteristics of the outer valence molecular orbitals. The experimental data for the 8σ orbital display an energy dependence which suggests that photoionization from this orbital may be influenced by the chlorine 3p Cooper minimum. The extent to which the 8σ orbital can be considered as a chlorine atom lone-pair is discussed. Vibrational structure has been observed in the [Xtilde] 2Π, Ã 2Σ+ and [Btilde] 2Π photoelectron bands recorded with HeI radiation, and has been assigned to progressions involving the ν+ 1 and ν+ 3 modes.

Gas-Phase Characterization of an Unhindered Germaimine by UV-Photoelectron Spectroscopy

An unhindered germaimine has been generated and characterized by the coupling of flash vacuum pyrolysis of two different precursors with UV-photoelectron spectroscopy. The Ge=N unit exhibits two ionizations in the low-energy region, corresponding to the ejection of an electron from the nitrogen atom lone pair and from the πGe=N orbital, respectively.

Adsorption and Thermal Behavior of Benzotriazole Chemisorbed on γ-Al2O3

Adsorption experiments for benzotriazole, (BTAH) on the γ-Al2O3 surface were carried out at 150 and 293 K. The thermal stability of the adsorbed layer was investigated. At low temperatures, adsorption results in the production of a thick condensed layer of BTAH. Strong intermolecular hydrogen bonds are observed. With increasing sample temperature, the BTAH molecules diffuse into the Al2O3 pore structure. Hydrogen bonding of the BTAH molecule specifically to isolated Al−OH groups is observed. Deprotonation of the BTAH molecule begins to occur through interaction, with the surface oxide anions near 300 K. As a result of such deprotonation-type interaction the production of associated surface OH groups and of the BTA- anion are observed. The BTA- anion is bound to the surface Lewis acid site via a nitrogen atom lone pair. Extensive thermal treatment (T = 573−623 K) causes decomposition of the adsorbed BTA- species, and modes related to the nitrogen ring disappear. After thermal treatment up to 873 K, IR spec...

Effect of Ring Size or an Additional Heteroatom on the Potency and Selectivity of Bicyclic Benzylamine-Type Inhibitors of PhenylethanolamineN-Methyltransferase1a

In the search for potent and selective inhibitors of the enzyme phenylethanolamine N-methyltransferase (PNMT; EC 2.1.1.28), we examined the effect of ring size or an additional heteroatom in the conformationally-restricted benzylamine-type PNMT inhibitors. Based on semiempirical calculations (MNDO) and molecular modeling studies, PNMT-inhibitory activity of these compounds seemed to be dependent on (a) the torsion angle between the plane of the aromatic ring and the endo N atom lone pair ( tau 2 angle), with the optimal value of tau 2 being about - 75 degrees, and (b) the amount of steric bulk about the 3-position of 1,2,3,4-tetrahydroisoquinoline (5, THIQ). 2,3,4,5-Tetrahydro-1H-2-benzazepine (6) was found to have the highest selectivity (PNMT Ki = 3.34 microM, alpha 2 Ki = 11 microM, selectivity = 3.2) as compared to other homologues of THIQ (PNMT Ki = 9.67 microM, alpha 2 Ki = 0.35 microM, selectivity = 0.036). The higher PNMT-inhibitory activity of 6 was attributed to favorable steric interactions of the puckered methylene groups in the putative bioactive conformation of 6 at the PNMT active site, whereas unfavorable interactions of these puckered methylene groups at the alpha 2-adrenoceptor were thought to be the cause of reduced alpha 2 affinity of 6. No further enhancement of the selectivity of the benzazepine ring system could be obtained via introduction of a second heteroatom (N, O, S) at the 5-position in this ring system.

Synthesis and pharmacological activity of a macrocyclic benzamide

a macrocyclic benzamide was synthesized and its affinities for 5-HT 3, 5-HT 4 and D 2 receptors were evaluated in binding assays. It was compared to reference benzamldes possessing a piperidine ring with varlous orlentations of the N-substituent. It was clearly demonstrated that the orientation of the basic nitrogen atom lone pair is an essential structural parameter in the recognition of 5-HT 3 and 5-HT 4 receptors.

Solid state structures of [hydrotris(3-tert-butyl-5-methylpyrazolyl)borato]chlorotin and -cadmium. Stereochemical influence of a central atom lone pair

The complexes [HB(3-Bu t -5-Mepz) 3 ] SnCl and [HB(3-Bu t pz) 3 ]CdCl(pz=pyrazolyl ring) have been prepared and their solid-state structures determined ciystallographically. The two structures allow a determination of the impact of the lone pair on ligand geometry and on the metal-donor atom distances for two metals with equivalent ionic radii. The geometry about tin in [HB(3-Bu t -5-Mepz) 3 ] SnCl is best described as a distorted trigonal bipyramid with the chloride ligand in an axial site and the tin lone pair occupying an equatorial position

Ab initio calculation of the structural parameters, conformational stability, vibrational frequencies and Raman and infrared intensities of methoxydimethylphosphine

The structural parameters of the near-cis (where the methyl moiety of the methoxy group is nearly eclipsing the lone pair on the phosphorus atom) and the trans (methoxymethyl with a dihedral angle of 180° from the phosphorus lone pair) conformations of methoxydimethylphosphine, CH 3OP(CH 3) 2, have been calculated with the RHF/3-21G ∗ and RHF/6-31G ∗ basis sets. For the smaller basis set the trans conformer is calculated to be more stable by 128 cm −1 (366 cal mol −1) than the near-cis rotamer, whereas with the 6-31G ∗ basis set the near-cis conformer is more stable than the trans conformer by 549 cm −1 (1570 cal mol −1). This latter result is consistent with the previously reported vibrational data for the vapor where predominately one conformer was observed. With the 6-31G ∗ basis set the near-cis rotamer has the methoxymethyl group rotated by 20° from eclipsing the phosphorus atom lone pair with a near-cis to near-cis barrier of 10 cm −1. Full optimization was also performed at the near-cis/trans transitional state and the barrier was calculated to be 1405 cm −1 (4.02 kcal mol −1) and 1675 cm −1 (4.77 kcal mol −1) with the 3-21G* and 6-31G* basis sets respectively. The force constants, vibrational frequencies, potential energy distributions, and the IR and Raman intensity parameters for both stable conformers were calculated with the 3-21G* basis set. These data are used to provide definitive assignments for the normal modes for both stable confonners.