Unconventional H‐bonds: SH···N interaction

Quantum calculations at the MP2/aug‐cc‐pVDZ level are used to analyze the SH···N H‐bond in complexes pairing H₂S and SH radical with NH₃, N(CH₃)₃, NH₂NH₂, and NH₂N(CH₃)₂. Complexes form nearly linear H‐bonds in which the S? H covalent bond elongates and shifts its stretching frequency to the red. Binding energies vary from 14 kJ/mol for acceptor NH₃ to a maximum of 22 kJ/mol for N(CH₃)₃ and N(CH₃)₂NH₂. Analysis of geometric, vibrational, and electronic data indicate that the SH···N interaction involving SH is slightly stronger than that in which the closed‐shell H₂S serves as donor. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A theoretical study of the condensation reactions of methyl cation with ammonia,water, hydrogen fluoride and hydrogen sulphide

Ab initio molecular orbital calculations have been used to study the condensation reactions of CH₃^? with NH₃, H₂O, HF and H₂S. Geometry optimization has been carried out at the Hartree—Fock (HF) level with the split-valence plus d-polarization 6-31G* basis set and improved relative energies obtained from calculations which employ the split-valence plus dp-polarization 6-31G** basis set with electron correlation incorporated via Moller—Plesset perturbation theory terminated at third order (MP3). Zero-point vibrational energies have also been determined and taken into account in deriving relative energies. The structures of the intermediates CH₃XH^? (X = NH₂, OH, F and SH) have been obtained and dissociation of these intermediates into CH₂X⁺ + H₂ on the one hand, and CH₃^? + HX on the other, has been examined. It is found that for those species for which the methyl condensation reaction is observed to have an appreciable rate (X = NH₂ and SH), the transition structure for hydrogen elimination from CH₃XH^? lies significantly lower in energy than the reactants CH₃^? + HX (by 75 and 70 kJ mol^?1 respectively). On the other hand, for those species for which the methyl condensation reaction is not observed (X = OH and F), the transition structure for H₂ elimination lies higher in energy than CH₃^? + HX (by 6 and 87 kJ mol^?1 respectively).     

Mechanism of Ethylene Migratory Insertion and Dimerization Catalyzed by δ‐Alkyl Platinum Complexes–A DFT Study

The mechanism of ethylene insertion reactions catalyzed by cationic δ‐alkyl platinum complexes has been studied at the B3LYP level of density functional theory. The initial steps of the reactions proceed via the coordination of ethylene to the reactants L₂Pt(II)R⁺, where L₂=none, (NH₃)₂, (CHNH)₂; R=H, CH₃, C₂H₅ in which ethylene coordinates strongly to the complexes PtCH⁺₃ and PtC₂H⁺₅ (coordination energies (CE) are 296.52 and 229.28 kJ/mol, respectively), while nitrogen‐containing ligands decrease the energies: Pt(NH₃)₂CH⁺₃ (CE: 180.04 kJ/mol), Pt(NH₃)₂C₂H⁺₅ (CE: 97.86 kJ/mol), Pt(CHNH)₂CH⁺₃ (CE : 176.31 kJ/mol) and Pt(CHNH)₂C₂H⁺₅ (CE: 91.00 kJ/mol). Moreover, ethylene insertion into the Pt‐alkyl bond, which is the rate‐determining step, is endothermic with barrier heights for L₂PtCH₃(C₂H₄)⁺ decreasing in the order: PtCH⁺₃ (164.18 kJ/mol)>(NH₃)₂ PtCH⁺₃ (129.95 kJ/mol)>(CHNH)₂ PtCH⁺₃ (115.27 kJ/mol), which has the same tendency for the ethyl case. The insertion product will continually undergo β‐hydride elimination, which is exothermic. On the other hand, the effects of solvent (dichloromethane, THF and benzene) are investigated with PCM method, but the inclusion of the effects in the computations only slightly affects the results. Beside that, a complete catalytic cycle for ethylene dimerization is studied in detail and the calculations agree well with known energetic and recognized tendencies.     

Theoretical investigation on identical anionic halide‐exchange SN2 reaction processes on N‐haloammonium cation NH3X+ (X = F,Cl, Br,and I)

CCSD(T) calculations have been used for identically nucleophilic substitution reactions on N‐haloammonium cation, X^? + NH₃X⁺ (X = F, Cl, Br, and I), with comparison of classic anionic S_N2 reactions, X^? + CH₃X. The described S_N2 reactions are characterized to a double curve potential, and separated charged reactants proceed to form transition state through a stronger complexation and a charge neutralization process. For title reactions X^? + NH₃X⁺, charge distributions, geometries, energy barriers, and their correlations have been investigated. Central barriers ΔE for X^? + NH₃X⁺ are found to be lower and lie within a relatively narrow range, decreasing in the following order: Cl (21.1 kJ/mol) > F (19.7 kJ/mol) > Br (10.9 kJ/mol) > I (9.1 kJ/mol). The overall barriers ΔE relative to the reactants are negative for all halogens: ?626.0 kJ/mol (F), ?494.1 kJ/mol (Cl), ?484.9 kJ/mol (Br), and ?458.5 kJ/mol (I). Stability energies of the ion–ion complexes ΔE_comp decrease in the order F (645.6 kJ/mol) > Cl (515.2 kJ/mol) > Br (495.8 kJ/mol) > I (467.6 kJ/mol), and are found to correlate well with halogen Mulliken electronegativities (R² = 0.972) and proton affinity of halogen anions X^? (R² = 0.996). Based on polarizable continuum model, solvent effects have investigated, which indicates solvents, especially polar and protic solvents lower the complexation energy dramatically, due to dually solvated reactant ions, and even character of double well potential in reactions X^? + CH₃X has disappeared. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical studies of the geometries of H2GeNaF and its insertion reaction with R?H (RF,OH, NH2, CH3)

The geometries and insertion reactions of germylene H₂GeNaF with R? H (R?F, OH, NH₂, CH₃) have been investigated at the B3LYP/6‐311+G level of theory. The potential barriers of the four reactions are ～52, 120, 184, and 257 kJ/mol, including the ZPVE corrections, respectively. Here, all the mechanisms of the four reactions are identical to each other; i.e., an intermediate has been located during the insertion reaction. The intermediate could dissociate into substituted germylane and NaF with the barrier corresponding to the dissociation energy. Correspondingly, the reaction energies for the four reactions are ?43, ?4, 21, and 51 kJ/mol, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

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.     

Theoretical studies on the alkylidene germylenoid H<Subscript>2</Subscript>C=GeLiF and its insertion reaction with R-H (R = F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>)

The geometries and isomerization of the alkylidene germylenoid H₂C=GeLiF as well as its insertion reactions with R-H (R = F, OH, NH₂, CH₃) have been systematically investigated at the B3LYP/6-311+ G* level of theory. The potential barriers of the four insertion reactions are 110.6, 145.0, 179.4, and 250.6 kJ/mol, respectively. Here, all the mechanisms of the four reactions are identical to each other, i.e., an intermediate has been formed first during the insertion reaction. Then, the intermediate could dissociate into the substituted germylene (H₂C=GeHR) and LiF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are 43.6, 78.8, 113.5, and 128.0 kJ/mol, respectively. Compared with the insertion reaction of H₂C= Ge∶ and R-H, the introduction of LiF makes the insertion reaction occur more difficultly. Furthermore, the effects of halogen (F, Cl, Br) substitution and inorganic salts employed on the reaction activity have also been discussed. As a result, the relative reactivity among the four insertion reactions should be as follows: H-F > H-OH > H-NH₂ > H-CH₃.     

Probing the imine silylenoid HN=SiNaF and its insertions reaction with R–H (R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>) using DFT

The geometries and isomerization of the imine silylenoid HN=SiNaF as well as its insertion reactions with some R–H molecules have been systematically investigated theoretically, where R=F, OH, NH₂, and CH₃, respectively. The barrier heights for the four insertion reactions are 67.7, 115.6, 153.5, and 271.5 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. Here, all the mechanisms of the four reactions are identical to each other, i.e., a stable intermediate has been formed during the insertion reaction. Then, the intermediate could dissociate into the substituted silylene (HN=SiHR) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are 71.8, 95.5, 123.3, and 207.6 kJ/mol, respectively, which are linearly correlated with the calculated barrier heights. Furthermore, the effects of halogen substitutions (F, Cl, and Br) on the reaction activity have also been discussed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

DFT studies of the phosphinidene derivative HPNaF and its insertion reaction with R–H(R=F,OH, NH<Subscript>2</Subscript>, CH<Subscript>3</Subscript>)

The formations of the phosphinidene derivative HPNaF and its insertion reactions with R–H (R=F, OH, NH₂, CH₃) have been systematically investigated employing the density functional theory (DFT), such as the B3LYP and MPW1PW91 methods. A comparison with the results of MP2 calculations shows that MPW1PW91 underestimates the barrier heights for the four reactions considered. Similarly, the same is also true for the B3LYP method depending on the selected reactions, but by much less than MPW1PW91, where the barrier heights of the four reactions are 25.2, 85.7, 119.0, and 142.4 kJ/mol at the B3LYP/6-311+G* level of theory, respectively. All the mechanisms of the four reactions are identical to each other, i.e., an intermediate has been located during the insertion reaction. Then, the intermediate could dissociate to substituted phosphinidane(H₂RP) and NaF with a barrier corresponding to their respective dissociation energies. Correspondingly, the reaction energies for the four reactions are −92.2, −68.1, −57.2, and −44.3 kJ/mol at the B3LYP/6-311+G* level of theory, respectively, where both the B3LYP and MPW1PW91 methods underestimate the reaction energies compared with the MP2 results. The linear correlations between the calculated barrier heights and the reaction energies have also been observed. As a result, the relative reactivity among the four insertion reactions should be as follows: H–F > H–OH > H–NH₂ > H–CH₃.     

Ab initio calculations of activation energy of the reaction of hydrogen exchange on strongly acidic centers

Ab initio calculations of fragments of the potential energy surfaces of hydrogen exchange reactions between H₂, CH₄, and alanine molecules and the H₃O⁺ ion were performed by the restricted Hartree-Fock method, at the second-order Møller-Plesset level of perturbation theory, and by the method of coupled clusters using the 6–31G^* and aug-cc-pVDZ basis sets. The one-center synchronous mechanism of hydrogen exchange reaction was studied and the activation energies and structures of transition states were determined. It was found that the geometric parameters of the H₂ and CH₄ molecules in the transition states are close to those of the H₃ ⁺ and CH₅ ⁺ ions. The higher the proton affinity of the reacting molecule in the reaction studied the lower the activiation energy of hydrogen exchange. The one-center mechanism studied can be used to describe the high-temperature solid-state catalytic isotope exchange (HSCIE) reaction. The results ofab initio calculations of synchronous hydrogen exchange between the H₃O⁺ ion and hydrogen atoms in different positions of the alanine molecule are in good agreement with experimental data on the regioselectivity and stereoselectivity of the HSCIE reaction with spillover-tritium.     

Calculation and properties of non-orthogonal,strictly local molecular orbitals

A general procedure to calculate non-orthogonal, strictly local molecular orbitals (NOLMOs) expanded using only a subset of the total basis set is presented. The energy of a single determinant wave function is minimised using a Newton-Raphson approach. Total energies and barriers to internal rotation for CH₄, NH₃, H₂O, CH₃CH₃, CH₃NH₂, CH₃OH, NH₂NH₂, NH₂OH and HOOH, and certain properties of the NOLMOs present in these molecules, are investigated using the 4-31G basis set.     

Degenerate lithium-hydrogen exchange reactions: Ab initio models for metallation mechanisms involving H2, CH4, NH3, H2O,and HF

Hydrogen exchange reactions between lithium and sodium compounds, MX (M=Li: X=H, CH₃, NH₂, OH, F; M=Na: X=CH₃), and the corresponding hydrides, HX, have been modelled by means of ab initio calculations including electron correlation and zero point energy (ZPE) corrections. Small or no activation barriers (from the initial complexes) are encountered in systems involving lone pairs (10.8, 2.4, 0.0 kcal/mol for X=NH₂, OH, F, respectively). Since the association energies of the initial complexes are much larger (21.0, 20.4, 23.5 kcal/mol, respectively; MP2/6–31+G*/6–31+G* + ZPE), such exchange reactions should occur spontaneously in the gas phase. The methyl systems (X=CH₃) have the largest barriers: 26.7 (M=Li) and 31.7 (M=Na) kcal/mol (MP2/6–31+G*/6–31G* + ZPE), and the initial complexes are only weakly bound. The significance of these systems as models for hydrogen exchange reactions in complexes of electropositive transition metals is discussed. However, the gegenion-free exchange of hydrogen between CH₃ and CH₄ has a much lower, 11.8 kcal/mol barrier (MP2/6–31+G*/6–31+G* + ZPE). All the transition structures are highly ionic (charges on the metals > +0.8). The effect of aggregation has been considered by examining the hydrogen exchange between (LiX)₂ and HX(X=H, CH₃, NH₂, OH). Although these dimer reactions formally involve six, instead of four electrons, no “aromatic” preference is observed.     

Study of the interaction between aniline and CH3CN, CH3Cl and CH3F

A computational study of dimers formed by aniline and one or two CH₃X molecules, X being CN, Cl or F, was carried out to elucidate the main characteristics of the interacting systems. Two different structures were found for each of the dimers, depending on the relative location of the CH₃X molecule with respect to the NH₂ hydrogen atoms. The most stable complex is formed with acetonitrile, with a complexation energy amounting to ?27.0?kJ/mol. Methyl chloride and methyl fluoride form complexes with complexation energies amounting to ?18.1 and ?17.5?kJ/mol, respectively, though the structural arrangement is quite different for both structures. In most complexes, the leading contribution to the stabilization of the complex is dispersion, though the electrostatic contribution is almost as important. Three different minima were obtained for clusters containing two CH₃X molecules depending on the side they occupy with respect to the phenyl ring. The complexation energies for these structures amount to ?58.5, ?38.6 and ?36.3?kJ/mol for acetonitrile, methyl chloride and methyl fluoride, respectively.     

Doubly excited configurations in modified CNDO and INDO methods

The effect of different CI basis sets, including doubly excited configurations, on transition energies calculated by modified CNDO and INDO methods is examined for H₂O, NH₃, CH₄, and H₂CO.     

Theoretical study on the isomerization and tautomerism in barbituric acid

Isomerization and tautomerism of 16 isomers of barbituric acid (BA) were studied at the MP2 and B3LYP levels of theory. Activation energies (E _a), imaginary frequencies (υ), and Gibbs free energies (ΔG ^#) of the amine-imine and keto-enol tautomerisms and O–H internal rotations were calculated. The activation energies of amine-imine tautomerisms were in the range of 110–200 kJ/mol and for keto-enol tautomerisms were larger than 200 kJ/mol. The calculated activation energies of internal O–H rotations were smaller than 60 kJ/mol. Effect of micro-hydration on the transition state structures and activation energies of the tautomerisms were also investigated. Water molecule catalyzed the tautomerisms and decreased the activation energies of both the amine-imine and keto-enol tautomerisms about 100–120 kJ/mol.     

Conformers of dehydrogenated glycine isomers

We report a comprehensive ab initio investigation of the conformers of dehydrogenated glycine radicals using the STO-3G, 3-21G, and aug-cc-pVDZ (aVDZ) basis sets and the UHF and UMP2 (H₂N-CH-COOH and HN-CH₂-COOH) as well as MCSCF and MRCI (H₂N-CH₂-COO) methods via two different conformational search strategies generating initial structures for optimizations by (a) removing H atoms from glycine conformers and (b) scanning torsional angles describing internal rotation along the C C, C N, and C O (except for H₂N-CH₂-COO) bonds of the radicals. We find four H₂N-CH-COOH {In_CH, IIn_CH, IIIn_CH, IVn_CH} and seven HN-CH₂-COOH {Ip_NH, IIp_NH, IIIn_NH, IVp_NH Vn_NH, VIp_NH, VIIp_NH} conformers with classical(adiabatic) relative energies of {0.00(0.00), 1.57(1.55), 5.25(5.03), 9.85(9.72)} and {0.00(0.00), 0.78(1.06), 1.93(2.08), 3.34(3.16), 3.39(3.29), 5.00(4.86), 9.27(8.87)} kcal/mol, respectively, obtained with UCCSD(T)-F12b/aug-cc-pVTZ(+UCCSD(T)-F12b/aVDZ ZPE correction) and four H₂N-CH₂-COO {Ip_COO, IIn_COO, IIIp_COO, IVn_COO} conformers with MRCI-F12+Q/aVDZ(+MRCI/aVDZ ZPE correction) energies of {0.00(0.00), 1.65(1.64), 1.78(1.75), 2.21(2.21)} kcal/mol, where n and p denote C₁ and C_s symmetry. The MRCI-F12+Q[UCCSD(T)-F12b] In_CH → Ip_NH and In_CH → Ip_COO classical(adiabatic) isomerization energies are 18.51(17.32)[21.20(20.01)] and 31.88(31.66) kcal/mol, respectively.     

Thermal decomposition of model compound of algal biomass

This contribution investigates thermal decomposition of leucine, as a representative model compound for amino acids in algal biomass. We map out potential energy surface for a wide array of unimolecular and self-condensation reactions operating in the decomposition of leucine. Decarboxylation and dehydration of leucine ensues by eliminating CO₂ and –OH, respectively, from the –COOH group attached to the α-carbon. The molecular channel for deamination involves cleavage of NH₂ from α-carbon of leucine. The activation energies for direct elimination of CO₂, NH₃, and H₂O from a leucine molecule lie within 20.7 kJ/mol of each other. Activation energies for these decomposition pathways reside below the bond dissociation enthalpy of H–C(α) of 323.1 kJ/mol. The decarboxylation, deamination, and dehydration pathways, via radical-prompted pathways, systematically require lower energy barriers, in reference to closed-shell reaction corridors. Detailed computations at the CBS-QB3 level provide the Arrhenius rate parameters for the unimolecular and bimolecular reactions, and standard enthalpies of formation, standard entropies, and heat capacities for all the products and intermediates. A kinetic analysis of gas-phase reactions, within the context of a plug-flow reactor model, accounts qualitatively for the formation of major products observed experimentally in the thermal degradation of the condensed-phase leucine. Among notable N-containing species, the model predicts the prevailing of NH₃ over HCN and HNCO, in addition to corresponding appreciable concentrations of amines, imines, and nitriles. Our detailed kinetic investigation illustrates a negligible contribution of the self-condensation reactions of leucine in the gas phase.     

1,2-Eliminations from (CH3)2NH+CH2CH3 and (CH3)2NH 2+ : Guided dissociations

1,2-Eliminations are a varied and extensive set of dissociations of ions in the gas phase. To understand better such dissociations, elimination of CH₂=CH₂ and CH₃CH₃ from (CH₃)₂NH⁺CH₂CH₃ (1) and of CH₄ from (CH₃)₂NH₂⁺ are characterized by quantum chemical calculations. Stretching of the CN bond to ethyl is followed by shift of an H from methyl to the bridging position in ethyl and then to N to reach (CH₃)₂NH₂⁺ + CH₂=CH₂ from 1. CH₃CH₃ elimination by H-transfer to C₂H₅⁺ to form CH₃NH⁺=CH₂ + CH₃CH₃ also takes place. (CH₃)₂NH₂⁺ eliminates methane by CN bond extension followed by β-H-transfer to give CH₂=NH⁺ + CH₄. Low-energy reactions resembling complex-mediated 1,2-eliminations occur and constitute a hitherto largely unrecognized type of reaction. As in many complex-mediated reactions, these reactions transfer H between incipient fragments. They are distinguished from complex-mediated processes by the fragments not being able to rotate freely relative to each other near the transition state for reaction, as they do in complexes. Most 1,2-eliminations are ion-neutral complex-mediated, occur by the just described lower energy reactions, have 1,1-like transition states, or utilize highly asynchronous 1,2 transition states. All of these avoid synchronized 1,2-transition states that would violate conservation of orbital symmetry.     

Linear-free energy relationships in solid-state reactions: I. Reactions of cobalt acetate with substituted aniline hydrochlorides

Solid-solid reactions of anhydrous cobalt(II) acetate with various substituted aniline hydrochlorides have been studied. The reaction products, CoCl₂(4-XC₆H₄NH₂)₂, where X = OCH₃, CH₃, F, Br, or Cl, have been characterized. The kinetics have been studied by noting the thickness of the colored boundary of the product. The values of energy of activation are 162.3, 148.6, 120.4, 102.9, and 104.6 kJ mole⁻¹ for X = OCH₃, CH₃, F, Br, and Cl, respectively. A plot of Hammett's constant σ versus log k is linear with values of ϱ 2.321, 2.012, 1.781, and 1.615 at 353, 358, 363, and 368 K, respectively.     

A simple,self-consistent electrostatic model for quantitative prediction of the activation energies of four-center reactions. II.*

A simple electrostatic model of point dipoles is used which permits direct calculation of the activation energies for the addition of the molecules H₂O, H₂S, H₃N, and H₃P to olefins. These calculated values agree with the known experimental data to within ±2 kcal/mole on the average. It was found that the best fit could be obtained with a polar transition state that corresponded to a reduction in bond order from 1 to ½ for the bond-breaking coordinates and an increase in bond order from 0 to 0.18 for the bond-forming coordinates. The replacement of a hydrogen atom of the species H₂O, H₂S, H₃N, or H₃P by a polarizable methyl group is expected to stabilize the charge on the central atoms. The following stabilization energies for the pairs H₂O? CH₃OH, H₂S? CH₃SH, H₃N? CH₃NH₂, H₃P? CH₃PH₂ were calculated: ?4.8 kcal/mole, ?0.7 kcal/mole, ?1.9 kcal/mole, ?0.8 kcal/mole, respectively.