Isomer and conformer selective atmospheric pressure chemical ionisation of dimethyl phthalate.

In this work we have studied the ionisation mechanism of Atmospheric Pressure Chemical Ionisation (ACPI) for three isomers of dimethyl phthalate (dimethyl phthalate - DMP (ortho- isomer), dimethyl isophthalate - DMIP (meta) and dimethyl terephthalate - DMTP (para)) using Ion Mobility Spectrometry (IMS) and IMS combined with an orthogonal acceleration Time of Flight Mass Spectrometer (oa-TOF MS). The molecules were chemically ionised using reactant ions H+·(H2O)n (n = 3 and 4). The positive IMS and IMS-oaTOF mass spectra of the isomers showed significant differences in the ion mobilities and in the ion composition. The IMS - oaTOF spectra consisted of clusters of ions M·H+·(H2O)n with different degrees of hydration (n = 0, 1, 2, 3) for different isomers. In the case of the DMP isomer, we have observed almost exclusive formation of M·H+ by proton transfer ionisation, while in the case of DMIP and DMTP, hydrated ions M·H+·(H2O)n (n = 1, 2, 3) and M·H+·(H2O)n (n = 0, 1, 2) respectively were detected, formed via adduct formation reactions. This behaviour was elucidated by differences in ionisation processes. In order to elucidate the ionisation processes we have carried out DFT calculations of the structures and energies of the neutral and protonated and hydrated isomers (for different conformers) and their corresponding proton affinities (PA) and hydration energies.

DFT Modeling of Cross-Linked Polyethylene: Role of Gold Atoms and Dispersion Interactions.

Using DFT modeling, we analyze the concerted action of gold atoms and dispersion interactions in cross-linked polyethylene. Our model consists of two oligomer chains (PEn) with 7, 11, 15, 19, or 23 carbon atoms in each oligomer cross-linked with one to three Au atoms through C-Au-C bonds. In structures with a single gold atom the C-Au-C bond is located in the central position of the oligomer. Binding energies (BEs) with respect to two oligomer radical fragments and Au are as high as 362-489 kJ/mol depending on the length of the oligomer chain. When the dispersion contribution in PEn-Au-PEn oligomers is omitted, BE is almost independent of the number of carbon atoms, lying between 293 and 296 kJ/mol. The dispersion energy contributions to BEs in PEn-Au-PEn rise nearly linearly with the number of carbon atoms in the PEn chain. The carbon-carbon distance in the C-Au-C moiety is around 4.1 Å, similar to the bond distance between saturated closed shell chains in the polyethylene crystal. BEs of pure saturated closed shell PEn-PEn oligomers are 51-187 kJ/mol. Both Au atoms and dispersion interactions contribute considerably to the creation of nearly parallel chains of oligomers with reasonably high binding energies.

Critical analysis of spectral solvent shifts calculated by the contemporary PCM approaches of a representative series of charge-transfer complexes between tetracyanoethylene and methylated benzenes.

Applications of contemporary polarisable continuum model (PCM) quantum chemical approaches to account for the solvent shifts of UV-Vis absorption charge transfer (CT) transitions in electron donor-acceptor (EDA) complexes (as well as to account for their stability and other properties in solvents) have been rather rare until now. In this study, we systematically applied different - mainly state-specific - PCM approaches to examine excited state properties, namely, solvatochromic excitation energy shifts in a series of EDA complexes of a tetracyanoethylene (TCNE) acceptor with methyl substituted benzenes with different degrees of methylation N (NMB). For these complexes, representative and reliable experimental data exist both for the gas phase and in solution (dichloromethane). We have found that the linear response (LR) solvent shifts are too small compared to the experimental values, while self-consistent SS approaches give values that are too large. The best agreement with experimental values was obtained by corrected LR (cLR). The transition energies were calculated by means of TD-DFT methodology with PBE0, CAM-B3LYP and M06-2X functionals as well as the wave function CC2 method for the gas phase, and the PCM solvent shifts were added to account for the solvent effects. The best results for transition energies in solvents were obtained using the CC2 method complemented by CAM-B3LYP/cLR for the gas phase transition energy red solvent shift, while all three TD-DFT approaches used gave insufficient values (ca. 50%) of the slope of the dependence of the transition energies on N compared to experimental values.

Theoretical study (CC2, DFT and PCM) of charge transfer complexes between antithyroid thioamides and TCNE: electronic CT transitions.

A set of representative DFT and wavefunction based theoretical approaches have been used to study ionization potentials and, predominantly, electronic charge transfer transitions in the complexes formed between TCNE as an electron acceptor and both mono and bicyclic thioamides as donors. The mentioned thioamides are of pharmacological importance due to their efficient antithyroid activity. Within a few kcal mol(-1) we have found six stable conformers for complexes with each of benzothioamides and four conformers for each of monocyclic thioamides. Present theoretical study satisfactorily shows that there is a good correspondence between the CC2/Def2-TZVPP calculated excitation energies for complexes in vacuum supplemented by the DFT solvent shifts and experiment. Present theoretical study contributes to deeper understanding of the electronic nature of the ground and excited states of the complexes with antithyroid activity.

DFT and MD study of the divalent-cation-mediated interaction of ochratoxin A with DNA nucleosides.

Aptamers are ligand-binding nucleic acids with affinities and selectivities that make them useful for the detection of a variety of compounds, including ochratoxin A. Theoretical methods can be applied to study the recognition interaction between aptamers and the ochratoxin A molecule. In this work, molecular dynamics simulations and quantum chemical calculations performed at the DFT level of theory were used to study the structures and energies of aptamers and aptamer-ochratoxin A complexes. The optimal structures as well as the interaction energies of these structures were elucidated. Divalent cations in the water solvent were shown to be an important influence on the structures and stabilities of the complexes.

Multiple anion...π interactions in tris(1,10-phenanthroline-κ(2)N,N')iron(II) bis[1,1,3,3-tetracyano-2-(2-hydroxyethyl)propenide] monohydrate.

In the ionic structure of the title compound, [Fe(C12H8N2)3](C9H5N4O2)2·H2O, the octahedral tris-chelate [Fe(phen)3](2+) dications [Fe-N = 1.9647 (14)-1.9769 (14) Å; phen is 1,10-phenathroline] afford one-dimensional chains by a series of slipped π-π stacking interactions [centroid-to-centroid distances = 3.792 (3) and 3.939 (3) Å]. The 1,1,3,3-tetracyano-2-(2-hydroxyethyl)propenide anions, denoted tcnoetOH(-), reveal an appreciable delocalization of π-electron density, involving the central propenide [C-C = 1.383 (3)-1.401 (2) Å] fragment and four nitrile groups, and this is also supported by density functional theory (DFT) calculations at the B97D/6-311+G(2d,2p) level. Primary noncovalent inter-moiety interactions comprise conventional O-H...O(N) and weak C-H...O(N) hydrogen bonding [O...O(N) = 2.833 (2)-3.289 (5) Šand C...O(N) = 3.132 (2)-3.439 (2) Å]. The double anion...π interaction involving a nitrile group of tcnoetOH(-) and two cis-positioned pyridine rings (`π-pocket') of [Fe(phen)3](2+) [N...centroid = 3.212 (2) and 3.418 (2) Å] suggest the relevance of anion...π stackings for charge-diffuse polycyanoanions and common M-chelate species.

Decafluorocyclohex-1-ene at 4.2†K - crystal structure and theoretical analysis of weak interactions.

The crystal structure of 1,2,3,3,4,4,5,5,6,6-decafluorocyclohex-1-ene (decafluorocyclohex-1-ene, C6F10) was solved in direct space from neutron powder diffraction data previously collected at 4.2 K [Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361] and refined by energy minimization in the solid state. To optimize the positions of the 64 atoms in the monoclinic computational cell the PBESOL and hybrid PBE0 functionals were used. The crystal structure of the title compound, which is liquid at room temperature, is built of antiparallel pairs of molecules assembled into molecular columns stacked along the a axis. Dominating the crystal-building forces are weak intermolecular dispersion interactions. Bonding conditions in the structure were analysed by theoretical molecular calculations of representative next-neighbor molecular dimers carried out using dispersion-corrected density functional theory (DFT) functionals and the SCS-MP2 wavefunction method. The largest interaction energy is of the order of ∼ 21 kJ mol(-1), above the interaction energy of a benzene dimer (11.3 kJ mol(-1)) and close to that of a water dimer (20.9 kJ mol(-1)). The interaction energy for the second most stable dimer can be compared with either that of a benzene dimer or of a C-H...π hydrogen bond. The remaining five weakly interacting dimers (∼ 4.2-8.4 kJ mol(-1)) can be characterized as having stronger interactions than those of methane dimers (-2.2 kJ mol(-1)), but weaker than those of benzene molecule pairs or weak C-H...C interactions for instance.

Theoretical study of electronic absorptions in aminopyridines - TCNE CT complexes by quantum chemical methods, including solvent.

The geometric and electronic structure of donor-acceptor complexes of TCNE with aniline, o-, m- and p- aminopyridines and pyridine has been studied in gas phase and in solution using CC2, TDDFT and CIS methods. Concerning interaction energy between particular donor and TCNE acceptor it is fairly described by both CC2 (MP2) and DFT-D approaches. Transition energies in gas phase calculated by CC2 approach are in good agreement with available experimental data for aniline. TDDFT calculations with LC-BLYP functional (with standard value of range separation factor µ = 0.47) gives transition energies too high although not as high as CIS. The red solvent shifts, calculated by PCM model with CIS method are qualitative correct, but error in the range of 0.1-0.2 eV should be expected.

Toluene dioxygenase mediated oxidation of halogen-substituted benzoate esters.

A series of ortho-, meta-, and para- halogen-substituted methyl benzoate esters was subjected to enzymatic dihydroxylation via the whole-cell fermentation with E. coli JM109 (pDTG601A). Only ortho-substituted benzoates were metabolized. Methyl 2-fluorobenzoate yielded one diol regioselectively whereas methyl 2-chloro-, methyl 2-bromo- and methyl 2-iodobenzoates each yielded a mixture of regioisomers. Absolute stereochemistry was determined for all new metabolites. Computational analysis of these results and a possible rationale for the regioselectivity of the enzymatic dihydroxylation is advanced.

Ethyl 1-ethyl-7-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylate: X-ray and DFT studies.

The basic building unit in the structure of the title compound, C(14)H(14)FNO(3), is pairs of molecules arranged in an antiparallel fashion, enabling weak C-H···O interactions. Each molecule is additionally involved in π-π interactions with neighbouring molecules. The pairs of molecules formed by the C-H···O hydrogen bonds and π-π interactions form ribbon-like chains running along the c axis. Theoretical calculations based on these pairs showed that, although the main intermolecular interaction is electrostatic, it is almost completely compensated by an exchange-repulsion contribution to the total energy. As a consequence, the dominating force is a dispersion interaction. The F atoms form weak C-F···H-C interactions with the H atoms of the neighbouring ethyl groups, with H···F separations in the range 2.59-2.80 Å.

Effects of finite size nuclei in relativistic four-component calculations of hyperfine structure.

The effect of a finite size model for both the nuclear charge and magnetic moment distributions on calculated EPR hyperfine structure have been studied using a relativistic four-component method based on density functional theory. This approach employs a restricted kinetically balanced basis (mDKS-RKB) and includes spin-polarization using noncollinear spin-density exchange-correlation functionals in the unrestricted fashion. Benchmark calculations have been carried out for a number of small molecules containing Zn, Cd, Ag, and Hg. The present results are compared with those obtained at the Douglas-Kroll-Hess second order (DKH-2) method. The dependence of the results on the quality of the orbital and auxiliary basis sets has been studied. It was found that some basis sets contain irregularities that deteriorate the results. Especial care has to be taken also on the construction of the auxiliary basis for fitting the total electron and spin-densities.

Theoretical study of structural changes caused by applying mechanical strain on peptide L24.

The influence of the mechanical strain on the artificial protein L(24) (acetyl-K(2)-L(24)-K(2)-amide) has been studied at the molecular mechanics (MM) level of theory. The effect of the surrounding environment (DPPC molecules) has been observed during the stretching or compressing of the L(24). The calculations gave the view on the structural changes occurring during these processes. All calculations were done using the GROMACS code with the ffgmx forcefield enhanced with lipid-protein interaction potentials.

Resonance electron capture by serine.

Formation of negative ions via dissociative electron attachment (DEA) to the amino acid serine in the gas phase was studied using two different crossed electron/molecular beam techniques and quantum chemical calculations. Resonance electron capture mass spectrum and effective ion yield curves of 16 negative ions were measured over the electron energy range from close to 0 to 11 eV. The negative ions from serine were detected from resonance states in the vicinity of 0, 1.3, 5, and 8 eV. The dominant reaction channel at low electron energies was (M-H)(-). The relative cross section for this ion exceeds more than 20 times that of any other fragment negative ions. A high-resolution experiment was applied to study fine structures in (M-H)(-) cross section. We have found that the second OH group influences some dissociative channels. Quantum chemical calculations were applied to interpret products of the DEA reaction channels.

(E)-Methyl 2-[(2-fluorophenyl)aminomethylene]-3-oxobutanoate: X-ray and density functional theory (DFT) study.

The title compound, C(12)H(12)FNO(3), a potential precursor for fluoroquinoline synthesis, is essentially planar, with the most outlying atoms displaced from the best-plane fit through all non-H atoms by 0.163 (2) and 0.118 (2) A. Molecules are arranged in layers oriented parallel to the (011) plane. The arrangement of the molecules in the structure is controlled mainly by electrostatic interactions, as the dipole moment of the molecule is 5.2 D. In addition, the molecules are linked by a weak C-H...O hydrogen bond which gives rise to chains with the base vector [1,1,1]. Electron transfer within the molecule is analysed using natural bond orbital (NBO) analysis. Deviations from the ideal molecular geometry are explained by the concept of non-equivalent hybrid orbitals.

2-anilinomethylene-3-oxobutanenitrile: an X-ray and density functional theory study.

Molecules of the title compound, C11H10N2O, are effectively planar. In the crystal structure, they are stabilized primarily by electrostatic interactions, as the dipole moment of the molecule is 4.56 D. In addition, the molecules are linked by weak C-H...N and C-H...O hydrogen bonds. An analysis of bonding conditions in the molecule was carried out using natural bond orbital (NBO) formalism.