Computational study toward understanding the photodissociation mechanism of sarin

The potential energy surface for sarin (C₄H₁₀FO₂P) dissociation into (CH₃)₂CHO+PO(F)(CH₃), CH₃+(CH₃)₂CHOPO(F), and F+(CH₃)₂CHOPO(CH₃) in the T₁ and S₁ states were investigated at the complete‐active‐space self‐consistent field (CASSCF) with the 6‐31G** and aug‐cc‐PVDZ basis sets. The different reaction pathways are characterized on the basis of the computed potential energy surface and surface crossing point, the time‐dependent density functional theory (TD‐DFT) was used to calculate the vertical energies based on the CAS(8,7)/6‐31G** optimized excited structures, which may provide some new insights into the mechanism of the ultraviolet photo‐degradation of sarin molecules. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

4,4′‐Bis(2,2,2‐trifluoroethoxymethyl)‐2,2′‐bipyridine

As part of a homologous series of novel polyfluorinated bipyridyl (bpy) ligands, the title compound, C₁₆H₁₄F₆N₂O₂, contains the smallest fluorinated group, viz. CF₃. The molecule resides on a crystallographic inversion centre at the mid‐point of the pyridine C_ipso—C_ipso bond. Therefore, the bpy skeleton lies in an anti conformation to avoid repulsion between the two pyridyl N atoms. Weak intramolecular C—H...N and C—H...O interactions are observed, similar to those in related polyfluorinated bpy–metal complexes. A π–π interaction is observed between the bpy rings of adjacent molecules and this is probably a primary driving force in crystallization. Weak intermolecular C—H...N hydrogen bonding is present between one of the CF₃CH₂– methylene H atoms and a pyridyl N atom related by translation along the [010] direction, in addition to weak benzyl‐type C—H...F interactions to atoms of the terminal CF₃ group. It is of note that the O—CH₂CF₃ bond is almost perpendicular to the bpy plane.     

MNDO Study of reaction pathways for SN2 reactions. Menschutkin reaction potential energy surfaces

MNDO molecular orbital calculations have been employed to investigate limited reaction pathways and potential energy surfaces for a series of S_N2 reactions. Model calculations for X^? + CH₃X (X = H, F, OH, OCH₃, and CN) indicate that the MNDO method gives qualitative agreement with ab initio studies except for the hydride–CH₄ exchange. Studies involving alkylation of pyridine (Menschutkin reaction) were also carried out. For the reaction of pyridine with CH₃Cl, which involves charge separation, our MNDO studies (which do not include solvation effects) do not produce a characteristic S_N2 pathway. For the reaction of pyridine with trimethyloxonium cation [(CH₃)₃O⁺] as the alkylating agent, a well defined S_N2 reaction pathway was obtained; this reaction involves charge transfer. A potential energy surface for the pyridine–trimethyloxonium cation reaction shows the presence of a saddle point transition state that resembles starting materials, in agreement with the Hammond postulate for this exothermic reaction.     

Electron driven processes in ices: Surface functionalization and synthesis reactions

The ability to control and orientate chemical reactivity in the condensed phase is a major challenge of modern research. Upon interaction with condensed molecules electrons drive bond cleavage thus generating a population of very reactive species in the condensed medium. These reactive species may interact either within the volume leading to the synthesis of new molecules or with the substrate surface by forming strong chemical bonds. The former reaction is known as electron induced synthesis and the latter one as electron induced surface functionalization.High-energy electrons achieve only a low chemical specificity due to the large number of dissociating open channels. In contrast, electrons with energies below ionization threshold of the irradiated matter are capable of high selectivity because of the dissociative electron attachment mechanism.In this review recent studies of electron interaction with condensed molecules on hydrogenated diamond substrates will be described. In particular electron induced functionalization of diamond surfaces by CH₂CN groups, decarboxylation reactions in condensed films of pure organic acids RCOOH (R = H, CH₃, C₂H₅, CF₃), carbamic acid formation in CO₂:NH₃, HCOOH:NH₃ and CF₃COOH:NH₃ binary ice mixtures, and glycine formation in a CH₃COOD:NH₃ mixture are presented and discussed.     

[4‐(Tri­fluoro­methyl)­phenyl]­aceto­nitrile

The crystal structure of the title compound, C₉H₆F₃N, at 123 K contains mol­ecules linked together via several C—H?F and C—H?N contacts, the strongest of which are 2.58 and 2.65 Å, respectively. Apparently, an F atom in the CF₃ group is able to compete with a cyano N atom for aromatic H atoms but is less prone to interact with the more acidic methyl­ene H atoms. The Ph–CH₂CN torsion angle is ?6.4 (2)° and the planar phenyl ring exhibits a typical deformation of the endo angles at the ipso‐C atoms, due to the difference in the electron‐withdrawing power of the CF₃ and CH₂CN substituents.     

Dispersion interactions between neighboring Bi atoms in (BiH3)2 and Te(BiR2)2

Triggered by the observation of a short Bi⋯Bi distance and a Bi Te Bi bond angle of only 86.6° in the crystal structure of bis(diethylbismuthanyl)tellurane quantum chemical computations on interactions between neighboring Bi atoms in Te(BiR₂)₂ molecules (R = H, Me, Et) and in (BiH₃)₂ were undertaken. Bi⋯Bi distances atoms were found to significantly shorten upon inclusion of the d shells of the heavy metal atoms into the electron correlation treatment, and it was confirmed that interaction energies from spin component‐scaled second‐order Møller–Plesset theory (SCS‐MP2) agree well with coupled‐cluster singles and doubles theory including perturbative triples (CCSD(T)). Density functional theory‐based symmetry‐adapted perturbation theory (DFT‐SAPT) was used to study the anisotropy of the interplay of dispersion attraction and steric repulsion between the Bi atoms. Finally, geometries and relative stabilities of syn–syn and syn–anti conformers of Te(BiR₂)₂ (R = H, Me, Et) and interconversion barriers between them were computed. © 2018 Wiley Periodicals, Inc.     

An ab initio molecular orbital study of the deprotonation of amines

The geometries of the amines NH₂X and amido anions NHX^?, where X = H, CH₃, NH₂, OH, F, C₂H, CHO, and CN have been optimized using ab initio molecular orbital calculations with a 4-31G basis set. The profiles to rotation about the N? X bonds in CH₃NH^?, NH₂NH^?, and HONH^? are very similar to those for the isoprotic and isoelectronic neutral compounds CH₃OH, NH₂OH, and HOOH. The amines with unsaturated bonds adjacent to the nitrogen atoms undergo considerable skeletal rearrangement on deprotonation such that most of the negative charge of the anion is on the substituent. The computed order of acidity for the amines NH₂X is X = CN > HCO > F ≈ C₂H > OH > NH₂ > CH₃ > H and for the reaction NHX^? + H⁺ → NH₂X the computed energies vary over the range 373–438 kcal/mol.     

Rebek Imide Platforms as Model Systems for the Investigation of Weak Intermolecular Interactions

A Rebek imide receptor with an acetylene‐linked phenyl ring complexes 2,6‐di(isobutyramido)pyridine in (CDCl₂)₂ via triple H‐bonding and π–π‐stacking interactions, and the influence of para‐substituents on both rings was investigated by ¹H NMR binding titrations. When the phenyl ring was extended to biphenyl and the C(4)‐pyridine substituent varied, interaction energies increased in the order CH₃CH₂???phenyl<CH₃S???phenyl<phenyl???phenyl?N‐methylcarboxamide???phenyl, highlighting the energetic gain from π stacking on amide fragments. The predicted preference of amide–π stacking for an antiparallel alignment of the local dipoles could not be confirmed with the studied system. Different substituents were introduced in the para position of the phenyl ring and their interaction with bound 2,6‐di(isobutyramido)pyridine was investigated. Theoretical predictions that the mere introduction of a substituent has a stabilizing effect on π–π stacking, regardless of its electronic nature, were experimentally confirmed.     

Noncovalent Interaction of Graphene with Heterocyclic Compounds: Benzene,Imidazole, Tetracene,and Imidazophenazines

Noncovalent functionalization of graphene with organic molecules offers a direct route to multifunctional modification of this nanomaterial, leading to its various possible practical applications. In this work, the structures of hybrids formed by linear heterocyclic compounds such as imidazophenazine (F1) and its derivatives (F2‐F4) with graphene and the corresponding interaction energies are studied by using the DFT method. Special attention is paid to the hybrids where the attached molecule is located along the graphene zigzag ( G_ZZ) and armchair ( G_AC ) directions. The interaction energies corresponding to the graphene hybrids of the F1‐F4 compounds for the two directions are found to be distinct, while tetracene (being a symmetrical molecule) shows a small difference between these binding energies. It is found that the back‐side CH₃ and CF₃ groups have an important influence on the arrangements of F1 derivatives on graphene and on their binding energies. The contribution of the CF₃ group to the total binding energy of the F3 molecule with graphene is the largest (3.4 kcal mol^?1) (the G_ZZ direction) while the CH₃ group increases this energy of F2 only by 2.0 kcal mol^?1 (the G_AC direction). It is shown that replacing the carbons with other atoms or adding a back‐side group enables one to vary the polarizability of graphene.     

Ab initio study of 4-monosubstituted pyrimidines in ground and excited n → π* states

Ab initio SCF and SCF -CI calculations have been performed to investigate substituent effects on ground- and excited-state properties of 4-R-pyrimidines, and to compare these with substituent effects in 2- and 4-R-pyridines, with R including the π donating and σ withdrawing groups CH₃, NH₂, OH, F, and C₂H₃ and the σ and π electron-withdrawing groups CHO and CN. Substitution leads to significant changes in the internal angles of the pyrimidine ring, which are independent of the nature of the substituent. The geometry of the pyrimidine ring is more sensitive to substitution in the 4 position than the pyridine ring geometry is to substitution in either the 2 or the 4 position. The isodesmic reaction energies for substituent transfer from the 4 position of pyrimidine to the 2 or 4 position of pyridine indicate that all R groups except CN have a relative stabilizing effect in pyrimidine. The presence of a π donating group leads to an increase in the n→π* transition energy of 4-R-pyrimidines, while the π withdrawing group CN leads to a decrease in the transition energy relative to pyrimidine. Orbital energy differences and virtual excitation energies tend to correlate with n→π* transition energies of 4-R-pyrimidines with saturated R groups, but such correlations are masked by π conjugation, n orbital interaction, and configurational mixing when the unsaturated groups C₂H₃, CHO, and CN are present. The electronic effects of a π donating group are stronger when the group is bonded to pyrimidine than to pyridine, but those of a π withdrawing group are weaker when the group is bonded to pyrimidine.     

Kinetic Parameters for Direct Atomic Substitution Reactions

Experimental data (the rate constants and activation energies) for seven reactions of direct substitution of one atom for another D + CH₃R CH₂DR + H, D + NH₃ DNH₂ + H, D + H₂O HOD + H, F + CH₃X CH₃F + X (X = F, Cl, Br, and I) involving atoms D and F and molecules C₂H₆, H₂O, NH₃, CH₃F, CH₃Cl, CH₃Br, and CH₃I are analyzed using the parabolic model of a bimolecular radical reaction. The activation energies for the thermally neutral analogs of these substitution reactions are calculated. Atomic substitution involving deuterium atoms has a lower activation energy of a thermally neutral reaction than radical abstraction or substitution.     

Carbene tetrel-bonded complexes

An ab initio calculation has been carried for the carbene tetrel bonded complexes CH₃Y???CH₂ (Y = F, CN, NC, and NO₂), CH₃F???CZ₂ (Z = Cl and CH₃), XH₃F???CF₂ (X = C, Si, Ge, and Sn), SiF₄???CF₂, and XH₃F???NHC (N-heterocyclic carbene), where carbene is treated as a Lewis base and XH₃Y is a Lewis acid. Formation of the tetrel bond is mainly attributed to charge transfer from the lone pair on the C atom in the carbene toward the σ* X–Y orbital and also the σ* X–H one in the strong tetrel bond. The carbene tetrel bond is strengthened/weakened by the electron-withdrawing group in the tetrel donor/acceptor and enhanced by the methyl group in C(CH₃)₂. NHC forms a stronger carbene tetrel bond in XH₃F???NHC (X = Si, Ge, and Sn) where it exceeds that of the majority of H-bonds. Interestingly, the tetrel bond becomes stronger in the order of X = C < Ge < Sn < Si in XH₃F???NHC and the largest interaction energy occurs in SiH₃F???NHC, amounting to ?103 kJ/mol. The carbene tetrel bond can be strengthened by cooperative effect with the N???M interaction in trimers H₂C???CH₃CN???M (M = CH₃CN, HCN, ICN, SbH₂F, LiCN, and BeH₂) and has doubled in H₂C???CH₃CN???BeH₂.

     

Synthesis,crystal structure and catalytic performance of bis (imino)pyridyl nickel complexes

Two new Ni(II) complexes of 2,6-bis[1-(2,6-diethylphenylimino)ethyl]pyridine (L¹), 2,6-bis[1-(4-methylphenylimino)ethyl]pyridine (L² ) have been synthesized and structurally characterized. Complex Ni(L¹)Cl₂?·?CH₃CN (1), exhibits a distorted trigonal bipyramidal geometry, whereas complex Ni(L¹)(CH₃CN)Cl₂ (2), is six-coordinate with a geometry that can best be described as distorted octahedral. The catalytic activities of complexes 1, 2, Ni{2,6-bis[1-(2,6-diisopropyl-phenylimino)ethyl]pyridine} Cl₂?·?CH₃CN (3), and Ni{2,6-bis[1-(2,6-dimethylphenylimino) ethyl]pyridine}Cl₂?·?CH₃CN (4), for ethylene polymerization were studied under activation with MAO.     

Oxide promoted isomerisation of an isonitrile complex,H2Os3(CO)10[CN(CH2)3Si(OEt)3]

The isomerisation of H₂Os₃(CO)₁₀[CN(CH₂)₃Si(OEt)₃] to HOs₃(CO)₁₀-[CN(H)(CH₂)₃Si(OEt)₃] is accelerated by interaction with some oxides; both complexes afford HOs₃(CO)₁₀[CN(H)(CH₂)₃Si(OEt)_3it-x(O)x] as oxide supported clusters.     

A first-principles investigation on interactions between various surface-terminated diamond films

To elucidate the influence of different terminations on diamond surface interaction, the geometry and electronic structures of the diamond films modified by different terminations (H, F, O, NH₂, and OH) are studied by using the first principles method. Strong bonding is formed between the clean diamond surfaces, which suggest an obvious interface interaction. Both H and F terminals have significant effects on the reduction of the interface interactions. Due to the larger difference in electronegativity between C and F, the F termination layer has a higher electron density coverage to give a larger repulsive force. Therefore, the interaction between the F-terminated diamond interfaces is stronger than that between the H-terminated diamond interfaces. The O-terminated diamond surfaces are unstable. The NH₂- and OH-terminals have weak interaction due to the presence of large functional group atoms that leads to an electronic offset.     

Investigating the nature of intermolecular and intramolecular bonds in noble gas containing molecules

This article presents a theoretical study on a number of selected noble gas containing systems of the general formula FNgR and NgR (Ng = He, Ne, Ar, Kr, Xe and R = CH₃, CN, CCH, BO, BNH, H, BeO, and AuF). The principal structures, bond energies, spectroscopic, and electronic properties of 28 noble gas containing molecules were investigated using density functional theory at the BMK level. Quantum theory of atoms in molecules, natural bond orbital, and several other analysis methods have been used to provide more insight into the nature of noble gas bonds. Although both F? Ng and Ng? R bonds in the investigated molecules are assigned to have partially covalent and partially electrostatic nature, the covalent character is dominant in Ng? R bonds. In the second part, the intermolecular interactions between FNgR molecules and hydrogen fluoride are overviewed with emphasis on the hydrogen bonding through the fluorine side of noble gas molecule with hydrogen of HF. The calculated interaction energies were found to decrease in magnitude going down the noble gas series. For all noble gases, the strongest hydrogen bond has been observed in the case R=CH₃. On the contrary, using R=CN in the FNgR moiety weakens the interaction strength. © 2014 Wiley Periodicals, Inc.     

Acetyldicyanmethanid-Komplexe einiger 3d-Metalle

Acetyldicyanomethanide Complexes of Some 3d-Metals . A series of mixed acetyldicyanomethanide amine complexes of some bivalent 3d-metals of the types [M(CH₃COC(CN)₂)₂py₄] and [M(CH₃COC(CN)₂)₂(amine)₂]; (M: Mn, Co, Ni, Cu, Zn; amine: pyridine, 2-, 4-methylpyridine) is reported. Infrared spectroscopic investigations are indicating, that the ambident acetyldicyanomethanide ligand shows an unusual variability of the preferred donor atom. O- or N-coordination of the monodentate anionic ligand in the tetra-pyridine complexes as well as a bridging function of the acetyldicyanomethanide ligand in the polymeric octahedral or distorted octahedral di-amine complexes preferrably with carbonyl-O and cyano-N as donor atoms is observed.     

13C relaxation times,T1, in six-coordinate cobalt(III) complexes: Study of the axial Co?N (heterocyclic) bond

Carbon-13 relaxation times, T₁, have been measured for ten cobalt(III)–cyclohexanedione dioxime complexes: CH₃CH₂? Co(Niox)₂-p-R-pyridine [R?H, N(CH₃)₂, CH₃, C₂H₅, C(CH₃)₃, Cl, Br, CN and COCH₃] and CH₃CH₂? Co(Niox)₂-3-N-methylimidazole. The values obtained have been rationalized by making assumptions on the length of the metal—hetrocyclic nitrogen bond. The internal rotation around the axial Co? N (heterocyclic) bond is faster for the 3-N-methylimidazole ligand than for the pyridine ligands. Correlations of the T₁ values with the σ-donor and π-acceptor character of the pyridine ligands were attempted. The interpretation of the results suggests the existence of π-back-bonding from the metal to the N-1 pyridine nitrogen atom, in agreement with the results of other workers. This conclusion, however, was not supported by the use of the para-C chemical shift as a criterion for back-bonding in pyridine–transition metal complexes.     

Metall-Pseudohalogenide. 29. Hexamethyl-phosphorsäuretriamid-Komplexe von 3d-Metall-tricyanmethaniden

Metal Pseudohalides. 29. Hexamethyl-phosphorusamide Complexes of Tricyanmethanides of 3d Metals The preparation of a series of new complexes of the types M(((CH₃)₂N)₃PO)₂(C(CN)₃)₂(M = Mn, Fe, Co, Ni, Cu, Zn) and of the complex Cu(((CH₃)₂N)₃PO)₄(C(CN)₃)₂ is reported. The structures of the compounds are discussed using infrared spectra and X-ray diagrams.     

Approximate transferability in alkanenitriles

The atomic and bond properties of a series of alkanenitriles were calculated in order to analyze the transferability of the CN, methyl, and methylene groups. The calculations were carried out using the atoms in molecules (AIM) theory on RHF/6‐31++G**// RHF/6‐31G** wave functions obtained for compounds CN–R (R ranging from H to C₁₁H₂₃). Linear correlations between L(Ω) and N(Ω) were used to establish N(CH₂) and N(CH₃) nearly transferable values. Average values and maximum differences to the mean value of several properties were used for classifying the CN group. It shows a transferable behavior along the CN–R series for R>Et. The methyl group presents specific properties when R<Pr. The methylene groups can be classified considering both their position with respect to the end of the chain and the position with respect to the CN group. The atomic energy displays a dependence on the molecular size. Although this behavior does not allow to consider this property as transferable, both the ab initio total electronic molecular energies and the experimental heats of formation can be fitted, by linear regression analysis, as a function of the number of methylene groups. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001