STM study of the conformation and reaction of long-chain haloalkanes at Si(111)-7 x 7

Scanning tunneling microscopy (STM) has been used to study the adsorption of 1-fluoro-, 1-chloro-, and 1-bromo-substituted C(12) alkanes at the Si(111)-7 x 7 surface, at temperatures from 300 to 500 K. We report self-assembly of these physisorbed adsorbates, C(12)H(25)X, to form approximately circular corrals, (C(12)H(25)X)(2), with charge transfer to a corralled adatom in each case (cf. Dobrin et al. Surf. Sci. 2006, 600, L43). The corrals comprised pairs of semicircular horizontal long-chain molecules stable to approximately 100 degrees C. At > or =150 degrees C, the corrals desorbed or reacted locally to imprint a halogen atom, X-Si, and an adjacent alkane residue, R-Si. The corral height profiles, together with the location of the imprinted X-Si resulting from thermal or electron-induced surface reaction, led to a picture of the molecular configurations in these haloalkane corrals, (C(12)H(25)X)(2), X = F, Cl, Br, and the dichloro corrals, 1,12-dichlorododecane, (ClC(12)H(24)Cl)(2).     

Theoretical study of samarium (II) carbenoid (ISmCH2I) promoted cyclopropanation reactions with ethylene and the effect of THF solvent on the reaction pathways

A computational study of the cyclopropanation reactions of divalent samarium carbenoid ISmCH(2)I with ethylene is presented. The reaction proceeds through two competing pathways: methylene transfer and carbometalation. The ISmCH(2)I species was found to have a "samarium carbene complex" character with properties similar to previously investigated lithium carbenoids (LiCH(2)X where X = Cl, Br, I). The ISmCH(2)I carbenoid was found to be noticeably different in structure with more electrophilic character and higher chemical reactivity than the closely related classical Simmons-Smith (IZnCH(2)I) carbenoid. The effect of THF solvent was investigated by explicit coordination of the solvent THF molecules to the Sm (II) center in the carbenoid. The ISmCH(2)I/(THF)(n)() (where n = 0, 1, 2) carbenoid methylene transfer pathway barriers to reaction become systematically lower as more THF solvent is added (from 12.9 to 14.5 kcal/mol for no THF molecules to 8.8 to 10.7 kcal/mol for two THF molecules). In contrast, the reaction barriers for cyclopropanation via the carbometalation pathway remain high (>15 kcal/mol). The computational results are briefly compared to other carbenoid reactions and related species.     

Density functional theory investigation of the reactions of isodihalomethanes (CH(2)X-X where X = Cl, Br, or I) with ethylene: substituent effects on the carbenoid behavior of the CH(2)X-X species

We investigated the chemical reactions of isodihalomethane (CH(2)X-X) and CH(2)X radical species (where X = Cl, Br, or I) with ethylene and the isomerization reactions of CH(2)X-X using density functional theory calculations. The CH(2)X-X species readily reacts with ethylene to give the cyclopropane product and an X(2) product via a one-step reaction with barrier heights of approximately 2.9 kcal/mol for CH(2)I-I, 6.8 kcal/mol for CH(2)Br-Br, and 8.9 kcal/mol for CH(2)Cl-Cl. The CH(2)X reactions with ethylene proceed via a two-step reaction mechanism to give a cyclopropane product and X atom product with much larger barriers to reaction. This suggests that photocyclopropanation reactions using ultraviolet excitation of dihalomethanes most likely occurs via the isodihalomethane species and not the CH(2)X species. The isomerization reactions of CH(2)X-X had barrier heights of approximately 14.4 kcal/mol for CH(2)I-I, 11.8 kcal/mol for CH(2)Br-Br, and 9.1 kcal/mol for CH(2)Cl-Cl. We compare our results for the CH(2)X-X carbenoids to results from previous calculations of the Simmons-Smith-type carbenoids (XCH(2)ZnX) and Li-type carbenoids (LiCH(2)X) and discuss their differences and similarities as methylene transfer agents.     

Ring-opening reactions induced by gold(I) of five- and four-coordinate palladium(II) and platinum(II) complexes containing tripodal or linear polyphosphines

The tripodal ligands NP(3)(tris[2-(diphenylphosphino)ethyl]amine) and PP(3)(tris[2-(diphenylphosphino)ethyl]phosphine), form five-coordinate [Pd(NP(3))X]X [X = Cl (1), Br (2)], [M(PP(3))X]X [M = Pd: X = Cl (4), Br (5), I (6); M = Pt, X = Cl (7), Br (8), I (9)] and four-coordinate[Pd(NP(3))I]I (3) complexes containing three fused rings around the metal. The interaction between Au(tdg)X (tdg = thiodiglycol; X = Cl, Br) or AuI and the respective ionic halo complexes 1-9 in a 1:1 stoichiometric ratio occurs via a ring-opening reaction with formation of the heterobimetallic systems PdAu(NP(3))X(3)[X = Cl (11), Br (12), I (13)], [MAu(PP(3))X(2)]X [M = Pd: X = Cl (14), Br (15), I (16); M = Pt: X = Cl (17), Br (18), I (19)]. The cations of complexes 17 and 18 were shown, by X-ray diffraction, to contain a distorted square-planar Pt(II) arrangement (Pt(P(2)P)X) where PP(3) is acting as tridentate chelating ligand and an almost linear PAuX moiety bearing the dangling phosphorus formed in the ring-opening process. PPh(3) coordinates to Au(I) and not to M(II) when added in excess to 14 and 17. Complexes 14-17 and [Pt(P(4))](BPh(4))(2) (10) (P4=linear tetraphosphine) also react with A(I), via chelate ring-openings to give MAu(2)(PP(3))X(4) [M = Pd: X = Cl (20), Br (21), I (22); M = Pt: X = Cl (23)] and [Pt(2)Au(2)(mu-Cl)(2)(mu-P(4))(2)](BPh(4))(4) (24), respectively.     

The periodic table and the intrinsic barrier in s(n)2 reactions

The identity S(N)2 reactions on nitrogen (see eq 3) with nucleophiles having the general structure H(n)()X(-) where X belongs to the group of nonmetallic elements which do not border the line separating them from the metallic elements (X = F, Cl, Br, I, O, S, Se, N, P, and C) were studied at the G2+ level. The results show that, similarly to the previously observed phenomenon for S(N)2 reaction on carbon (J. Am. Chem. Soc. 1999, 121, 7724), the Periodic Table, through the valence of the element X, controls the intrinsic barrier for the reaction. The average intrinsic barriers obtained for nitrogen substrates were 20, 27, 39, and 57 kcal/mol for the mono-, di-, tri-, and tetravalent X's, respectively. It is also concluded that the intrinsic barriers are similar for N- and C-based substrates and dimethyl substitution on both raises the intrinsic barrier by ca. 10 kcal/mol.     

An experimental and theoretical evaluation of the reactions of silver hyponitrite with phosphorus halides. In search of the elusive phosphorus-containing hyponitrites

In the reaction of F2PBr, F2P(O)Br, (C6F5)2PBr, (CH3)2P(S)Br, and (CH3)2P(O)Cl with silver hyponitrite (AgON=NOAg), nitrous oxide (N2O) and mu-oxo phosphorus species were obtained in all cases rather than the plausible hyponitrite alternative. Theoretical calculations of the geometries and expected decomposition pathways of the phosphorus-containing hypothetical hyponitrites were carried out at the B3LYP/6-311+G(2df)//B3LYP/6-31+G(d) level. The cis-hyponitrite, XON=NOX (X=PF2, OPF2), is predicted to concertedly decompose to N2 plus phosphorus-containing radicals (OPF2, O2PF2) or to N2O plus the mu-oxo phosphorus species, X-O-X, (X=PF2, OPF2) with the former pathway having a smaller activation barrier (4.6 kcal/mol, X=PF2; 10.5 kcal/mol, X=OPF2). On the other hand, trans-hyponitrite can only decompose to N2 plus the phosphorus-containing radicals, because there is a very high barrier for rearrangement to cis-hyponitrite. These results are in disagreement with experiment, because only the mu-oxo phosphorus species are observed. Reconciliation between experiment and theory is made for X=OPF2 when a silver cation is included in the calculations. In THF (as a model for neat F2P(O)Br), the silver cation is predicted to reverse the order of the two transition states through stronger interactions with the oxygen atoms in the transition state of the N2O-producing pathway. Thus, Ag(I) is predicted to be not only catalytic for X=OPF2 but also product-specific toward the mu-oxo products.     

The kinetics and equilibrium of the gas-phase reaction CH3CF2Br + I2 = CH3CF2I + IBr the C-Br bond dissociation energy in 1,1-difluorobromoethane

The kinetics and equilibrium of the gas-phase reaction of CH₃CF₂Br with I₂ were studied spectrophotometrically from 581 to 662°K and determined to be consistent with the following mechanism: A least squares analysis of the kinetic data taken in the initial stages of reaction resulted in log k₁ (M^?1 · sec^?1) = (11.0 ± 0.3) - (27.7 ± 0.8)/θ where θ = 2.303 RT kcal/mol. The error represents one standard deviation. The equilibrium data were subjected to a “third-law” analysis using entropies and heat capacities estimated from group additivity to derive ΔH_r° (623°K) = 10.3 ± 0.2 kcal/mol and ΔH_rr (298°K) = 10.2 ± 0.2 kcal/mol. The enthalpy change at 298°K was combined with relevant bond dissociation energies to yield DH°(CH₃CF₂ - Br) = 68.6 ± 1 kcal/mol which is in excellent agreement with the kinetic data assuming that E₂ = 0 ± 1 kcal/mol, namely; DH°(CH₃CF₂ - Br) = 68.6 ± 1.3 kcal/mol. These data also lead to ΔH_f°(CH₃CF₂Br, g, 298°K) = -119.7 ± 1.5 kcal/mol.     

DFT calculations, structural and spectroscopic studies on the products formed between IBr and N,N'-dimethylbenzoimidazole-2(3H)-thione and -2(3H)-selone

The NBO charge distribution calculated at DFT level on the [LEX](+) species [LE=N,N'-dimethylbenzoimidazole-2(3H)-thione (3) and -2(3H)-selone (4)(Scheme 1); X=I, Br] suggests that the most likely products from the reaction 3 of 4 and with IBr are the 10-X-2 charge-transfer (CT) adduct and the 10-Se-3 "T-shaped" hypervalent adduct featuring a linear Br--Se--I system, respectively. This prediction is confirmed by the synthesis, and X-ray diffraction analysis of 3.IBr (I) and 4.I(0.72)Br(1.28)(II). In particular II, is a 10-Se-3 "T-shaped" hypervalent adduct containing an almost linear X--Se--X system [X--Se--X 179.07(3) degrees, X=I(0.36)/Br(0.64)], which is roughly perpendicular to the average plane of the benzoimidazole moiety. The FT-Raman spectra of I and II agree very well with their structural features. In particular, the complexity of the FT-Raman spectrum of II reflects the disorder in the X-ray crystal structure of this compound.     

Relative Gibbs energies in solution through continuum models: effect of the loss of translational degrees of freedom in bimolecular reactions on Gibbs energy barriers

We present here a cell model for evaluating Gibbs energy barriers corresponding to bimolecular reactions (or processes of larger molecularity) in which a loss of translational degrees of freedom takes place along the reaction coordinate. With this model, we have studied the Walden inversion processes: Xa- + H3CXb --> XaCH3 + Xb- (X = F, Cl, Br, and I). In these processes, our model yields an increase of about 2.3-3.4 kcal/mol in Gibbs energy in solution corresponding to the loss of the translational degrees of freedom when passing from separate reactants to the TS in good agreement with experimental data. The corresponding value in the gas phase is about 6.7-7.1 kcal/mol. When the difference between these two figures is used to correct the results obtained by the standard UAHF implementation of the continuum model, the theoretical results are brought significantly closer to the experimental ones. This seems to indicate that for these reactions the parametrization used does not adequately introduce the increase in Gibbs energy corresponding to the constriction of the translational motion of the species along the reaction coordinate when passing from the gas phase to solution. Therefore, we believe that continuum models could perform much better if we released the parametrization process from the task of taking into account the constriction in translation motion in solution, which could be more adequately evaluated using the cell model proposed here, thus allowing it to focus on better reproducing all the remaining solvation effects.     

Regioselective haloaromatization of 1,2-bis(ethynyl)benzene via halogen acids and PtCl2. Platinum-catalyzed 6-pi electrocyclization of 1,2-bis(1'-haloethenyl)benzene intermediates

[reaction: see text] Treatment of 1,2-bis(ethynyl)benzene (1) with aqueous HX (X = Br, I) in hot 3-pentanone (100-105 degrees C, 2 h) afforded 1,2-bis(1'-haloethenyl)benzene species 2-Br and 2-I in 98% and 95% yields, respectively. The hydrochlorination of endiyne 1 failed to proceed at elevated temperature but was implemented efficiently by PtCl2 (5 mol %) in hot 3-pentanone (100 degrees C, 2 h) to give 1,2-bis(1'-chloroethenyl)benzene 2-Cl in 80% yield. In the presence of PtCl2 (5 mol %), these halides 2-Cl,2-Br, and 2-I were subsequently converted to 1-halonaphthalenes 3-Cl, 3-Br, and 3-I in the mother solution via sequential 6-pi electrocyclization and dehalogenation reactions. PtCl2 (5 mol %) also effected direct haloaromatization of endiyne 1 with HX (X = Cl, Br, I) and gave 1-halonaphthalenes 3-Cl, 3-Br, and 3-I in 64-71% yields. This investigation reports the scope and the regioselectivity of haloaromatization of various enediynes catalyzed by PtCl2.     

Bonding trends of thiosemicarbazones in mononuclear and dinuclear copper(I) complexes: syntheses, structures, and theoretical aspects

Reactions of copper(I) halides with a series of thiosemicarbazone ligands (Htsc) in the presence of triphenylphosphine (Ph(3)P) in acetonitrile have yielded three types of complexes: (i) monomers, [CuX(eta1-S-Htsc)(Ph3P)2] [X, Htsc = I (1), Br (2), benzaldehyde thiosemicarbazone (Hbtsc); I (5), Br (6), Cl (7), pyridine-2-carbaldehyde thiosemicarbazone (Hpytsc)], (ii) halogen-bridged dimers, [Cu2(mu2-X)2(eta1-S-Htsc)2(Ph3P)2] [X, Htsc = Br (3), Hbtsc; I (8), furan-2-carbaldehyde thiosemicarbazone (Hftsc); I (11), thiophene-2-carbaldehyde thiosemicarbazone (Httsc)], and (iii) sulfur-bridged dimers, [Cu2X2(mu2-S-Htsc)2(Ph3P)2] [X, Htsc = Cl (4), Hbtsc; Br (9), Cl (10), pyrrole-2-carbaldehyde thiosemicarbazone (Hptsc); Br (12), Httsc]. All of these complexes have been characterized with the help of elemental analysis, IR, 1H, 13C, or 31P NMR spectroscopy, and X-ray crystallography (1-12). In all of the complexes, thiosemicarbazones are acting as neutral S-donor ligands in eta()S or mu2-S bonding modes. The Cu...Cu separations in the Cu(mu2-X)2Cu and Cu(mu2-S)2Cu cores lie in the ranges 2.981(1)-3.2247(6) and 2.813(1)-3.2329(8) Angstroms, respectively. The geometry around each Cu center in monomers and dimers may be treated as distorted tetrahedral. Ab initio density functional theory calculations on model monomeric and dimeric complexes of the simplest thiosemicarbazone [H2C=N-NH-C(S)-NH2, Htsc] have revealed that monomers and halogen-bridged dimers have similar stability and that sulfur-bridged dimers are stable only when halogen atoms are engaged in hydrogen bonding with the solvent of crystallization or H2O molecules.     

Theoretical study of C-H and N-H sigma-bond activation reactions by titinium(IV)-imido complex. Good understanding based on orbital interaction and theoretical proposal for N-H sigma-bond activation of ammonia

The C-H sigma-bond activation of methane and the N-H sigma-bond activation of ammonia by (Me3SiO)2Ti(=NSiMe3) 1 were theoretically investigated with DFT, MP2 to MP4(SDQ), and CCSD(T) methods. The C-H sigma-bond activation of methane takes place with an activation barrier (Ea) of 14.6 (21.5) kcal/mol and a reaction energy (DeltaE) of -22.7 (-16.5) kcal/mol to afford (Me3SiO)2Ti(Me)[NH(SiMe3)], where DFT- and MP4(SDQ)-calculated values are given without and in parentheses, respectively, hereafter. The electron population of the CH3 group increases, but the H atomic population decreases upon going to the transition state from the precursor complex, which indicates that the C-H sigma-bond activation occurs in heterolytic manner unlike the oxidative addition. The Ti atomic population considerably increases upon going to the transition state from the precursor complex, which indicates that the charge transfer (CT) occurs from methane to Ti. These population changes are induced by the orbital interactions among the d(pi)-p(pi) bonding orbital of the Ti=NSiMe3 moiety, the Ti d(z2) orbital and the C-H sigma-bonding and sigma*-antibonding orbitals of methane. The reverse regioselective C-H sigma-bond activation which leads to formation of (Me3SiO)2Ti(H)[NMe(SiMe3)] takes place with a larger Ea value and smaller exothermicity. The reasons are discussed in terms of Ti-H, Ti-CH3, Ti-NH3, N-H, and N-CH3 bond energies and orbital interactions in the transition state. The N-H sigma-bond activation of ammonia takes place in a heterolytic manner with a larger Ea value of 19.0 (27.9) kcal/mol and considerably larger exothermicity of -45.0 (-39.4) kcal/mol than those of the C-H sigma-bond activation. The N-H sigma-bond activation of ammonia by a Ti-alkylidyne complex, [(PNP)Ti(CSiMe3)] 3 (PNP = N-[2-(PH2)2-phenyl]2-]) ,was also investigated. This reaction takes place with a smaller E(a) value of 7.5 (15.3) kcal/mol and larger exothermicity of -60.2 (-56.1) kcal/mol. These results lead us to predict that the N-H sigma-bond activation of ammonia can be achieved by these complexes.     

Theoretical study on the mechanism of Ni-catalyzed alkyl-alkyl Suzuki cross-coupling

Ni-catalyzed cross-coupling of unactivated secondary alkyl halides with alkylboranes provides an efficient way to construct alkyl-alkyl bonds. The mechanism of this reaction with the Ni/L1 (L1=trans-N,N'-dimethyl-1,2-cyclohexanediamine) system was examined for the first time by using theoretical calculations. The feasible mechanism was found to involve a Ni(I)-Ni(III) catalytic cycle with three main steps: transmetalation of [Ni(I)(L1)X] (X=Cl, Br) with 9-borabicyclo[3.3.1]nonane (9-BBN)R(1) to produce [Ni(I)(L1)(R(1))], oxidative addition of R(2) X with [Ni(I)(L1)(R(1))] to produce [Ni(III)(L1)(R(1))(R(2))X] through a radical pathway, and C-C reductive elimination to generate the product and [Ni(I)(L1)X]. The transmetalation step is rate-determining for both primary and secondary alkyl bromides. KOiBu decreases the activation barrier of the transmetalation step by forming a potassium alkyl boronate salt with alkyl borane. Tertiary alkyl halides are not reactive because the activation barrier of reductive elimination is too high (+34.7 kcal mol(-1)). On the other hand, the cross-coupling of alkyl chlorides can be catalyzed by Ni/L2 (L2=trans-N,N'-dimethyl-1,2-diphenylethane-1,2-diamine) because the activation barrier of transmetalation with L2 is lower than that with L1. Importantly, the Ni(0)-Ni(II) catalytic cycle is not favored in the present systems because reductive elimination from both singlet and triplet [Ni(II)(L1)(R(1))(R(2))] is very difficult.     

Effective monkey saddle points and berry and lever mechanisms in the topomerization of SF(4) and related tetracoordinated AX(4) species

The topomerization mechanisms of the SF(4) and SCl(2)F(2) sulfuranes, as well as their higher (SeF(4), TeF(4)) and isoelectronic analogues PF(4)(-), AsF(4)(-), SbF(4)(-), SbCl(4)(-), ClF(4)(+), BrF(4)(+), BrCl(2)F(2)(+), and IF(4)(+)), have been computed at B3LYP/6-31+G and at B3LYP/6-311+G. All species have trigonal bipyramidal (TBP) C(2)(v)() ground states. In such four-coordinated molecules, Berry rotation exchanges both axial with two equatorial ligands simultaneously while the alternative "lever" mechanism exchanges only one axial ligand with one equatorial ligand. While the barrier for the lever exchange in SF(4) (18.8 kcal mol(-1)) is much higher than that for the Berry process (8.1 kcal mol(-1)), both mechanisms are needed for complete ligand exchange. The F(ax)F(ax) and F(eq)F(eq) isomers of SF(2)Cl(2) have nearly the same energy and readily interconvert by BPR with a barrier of 7.6 kcal mol(-1). The enantiomerization of the F(ax)F(eq) chiral isomer can occur by either the Berry process (transition state barrier 8.3 kcal mol(-1)) or the "lever" mechanism via either of two C(s)() transition states, based on the TBP geometry: Cl(ax) <--> Cl(eq) or F(ax) <--> F(eq) exchanges with barriers of 6.3 and 15.7 kcal mol(-1), respectively. Full scrambling of all ligand sites is possible only by inclusion of the lever mechanism. Planar, "tetrahedral", and triplet forms are much higher in energy. The TBP C(3)(v) structures of AX(4) either have two imaginary frequencies (NIMAG = 2) for the X = F, Cl species or are minima (NIMAG = 0) for the X = Br, I compounds. These "effective monkey saddle points" have degenerate modes with two small frequencies, imaginary or real. Although a strictly defined "monkey saddle" (with degenerate frequencies exactly zero) is not allowed, the flat C(3)(v) symmetry region serves as a "transition state" for trifurcation of the pathways. The BPR mechanism also is preferred over the alternative lever process in the topomerization of the selenurane SeF(4) (barriers 5.9 vs. 12.1 kcal mol(-1)), the tellurane TeF(4) (2.1 vs. 6.4), and the interhalogen cations ClF(4)(+) (2.5 vs 14.8), BrF(4)(+) (4.7 vs. 11.3), BrF(2)Cl(2)(+) (14.6 vs. 17.4), and IF(4)(+) (1.4 vs. 6.0), as well as for the series PF(4)(-) (7.0 vs. 9.0), AsF(4)(-) (9.3 vs. 17.2), and SbF(4)(-) (3.8 vs. 5.3 kcal mol(-1)), all computed at B3LYP/6-311+G with the inclusion of quasirelativistic pseudopotentials for Te, I, and Sb. The heavier halogens increasingly favor the lever process, where the barrier (2.6 kcal mol(-1)) pertaining to the effective monkey saddle point (C(3)(v) minimum for SbCl(4)(-)) is less than that for the Berry process (8.2 kcal mol(-1)).     

Theoretical predictions of the initial decomposition steps of dimethylnitramine

The structures and energies of the reactants, products, and transition states of the initial steps in the gas-phase decomposition of dimethylnitramine (DMNA) have been determined by quantum chemical calculations at the B3LYP density-functional theory, MP2, and G2 levels. The pathways considered are NO2 elimination, HONO elimination, and nitro-nitrite rearrangement. The NO2 elimination is predicted to be the main channel of the gas-phase decomposition of DMNA in accord with experiment. The values of the Arrhenius parameters, log A=16.6+/-0.5 and Ea=40.0+/-0.6 kcal/mol, for the N-NO2 bond-fission reaction were obtained using a canonical variational theory with B3LYP energies and frequencies. The HONO-elimination channel has the next lowest activation energy of 44.7+/-0.5 kcal/mol (log A=13.6+/-0.5) and is characterized by a five-member transition-state configuration in which a hydrogen atom from one of the methyl groups is transferred to an oxygen atom of NO2. Tunneling contributions to the rate of this reaction have been estimated. The nitro-nitrite rearrangement reaction occurs via a transition state in which both oxygen atoms of NO2 are loosely bound to the central nitrogen atom, for which Rice-Ramsperger-Kassel-Marcus theory predicts log A=14.4+/-0.6 and Ea=54.1+/-0.8 kcal/mol.     

Transition states of the retro-ene reactions of allylic diazenes

[reaction: see text] Density functional theory studies of intramolecular retro-ene reactions of allyldiazenes show that the reaction is a concerted process involving a six-center cyclic transition state. The activation barriers for deazetization for X = H, Me, F, Cl, and Br (3a-e) are 2.4, 40.2, 22.3, 9.3, and 8.8 kcal/mol, respectively.     

Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

Dissociation energies of the Cu and Ag monohalides and of Ni monofluoride

Gaseous isomolecular equilibria of the type CuX + Ag = Cu + AgX, where X = F, Cl, Br, and I, were studied by effusion-beam mass spectrometry at elevated temperatures, and the differences between the dissociation energies of the CuX and AgX molecular species were determined with relatively high accuracy from thermochemical analysis of the equilibrium data. Analysis of literature data, plus new information on AgBr, yielded accurate values of D degrees 0 in kcal mol(-1) for CuF (102.0), AgCl (74.4), AgBr (66.4), and AgI (59.7), from which values were derived for AgF (81.5), CuCl (89.6), CuBr (79.2), and CuI (69.4), all +/-1 kcal mol(-1). The result is a consistent set of dissociation energies for all eight of the Cu and Ag monohalides that will be useful in checking the reliability of quantum chemical calculations for these molecular species containing elements of increasing atomic number. Also, the isomolecular exchange equilibrium between CuF and NiF was studied in a similar fashion, leading to D degrees 0(NiF) = 104.4 +/- 1.4 kcal mol(-1).     

Dihydrogen and methane elimination from adducts formed by the interaction of carbenium and silylium cations with nucleophiles

Stationary points for reactions R'R' 'HX(+) + YH --> [R'R' 'X-Y](+) + H(2) (I) and R'(CH(3))HX(+) + YH -->[R'HX-Y](+) + CH(4) (II) (R', R' ' = CH(3), H; X = C, Si; Y = CH(3)O, (CH(3))(2)N, and C(6)H(5)) are located and optimized by the B3LYP/aug-cc-pVDZ method. A similar mechanism was found to be operative for both types of reactions with X = C and X = Si. Formation of the intermediate (adduct) results in the transfer of electron density from the electron-rich bases to the X atoms and in the growth of a positive charge on a hydrogen atom attached to Y. This mobile proton may shift from Y to X, and the relative energies of transition states for elimination reactions (Delta) depend on the ability of the X atom to retain this proton. Therefore, Deltagrows on going from Si to C and with increasing numbers of methyl substituents. For X = C, the Deltavalue for both reactions correlates well with the population of the valence orbitals of X in a wide range from -44 kcal/mol (methyl cation/benzene) to 31 kcal/mol (isopropyl cation/methanol). For X = Si this range is more narrow (from -19 to -5.0 kcal/mol), but all Delta values are negative with the exclusion of silylium ion/benzene systems, adducts of which are pi- rather than sigma-complexes. The energy minima for product complexes for H(2) elimination are very shallow, and several are dissociative. However, complexes with methane which exhibit bonding between X and the methane hydrogen are substantially stronger, especially for systems with X = Si. The latter association energy may reach 8 kcal/mol (Si...H distance is 2 A).     

A Marcus treatment of rate constants for protonation of ring-substituted alpha-methoxystyrenes: intrinsic reaction barriers and the shape of the reaction coordinate

Rate and equilibrium constants were determined for protonation of ring-substituted -methoxystyrenes by hydronium ion and by carboxylic acids to form the corresponding ring-substituted alpha-methyl alpha-methoxybenzyl carbocations at 25 degrees C and I = 1.0 (KCl). The thermodynamic barrier to carbocation formation increases by 14.5 kcal/mol as the phenyl ring substituent(s) is changed from 4-MeO- to 3,5-di-NO2-, and as the carboxylic acid is changed from dichloroacetic to acetic acid. The Br?nsted coefficient alpha for protonation by carboxylic acids increases from 0.67 to 0.77 over this range of phenyl ring substituents, and the Br?nsted coefficient beta for proton transfer increases from 0.63 to 0.69 as the carboxylic acid is changed from dichloroacetic to acetic acid. The change in these Br?nsted coefficients with changing reaction driving force, (inverted theta)alpha/ (inverted theta) deltaG(av) degrees=(inverted theta)beta/(inverted theta)delta G(av) degrees= 1/8lambda = 0.011, is used to calculate a Marcus intrinsic reaction barrier of lambda= 11 kcal/mol which is close to the barrier of 13 kcal/mol for thermoneutral proton transfer between this series of acids and bases. The value of alpha= 0.66 for thermoneutral proton transfer is greater than alpha= 0.50 required by a reaction that follows the Marcus equation. This elevated value of beta may be due to an asymmetry in the reaction coordinate that arises from the difference in the intrinsic barriers for proton transfer at the oxygen acid reactant and resonance-stabilized carbon acid product.