Dimers of and tautomerism between 2-pyrimidinethiol and 2(1H)-pyrimidinethione: a density functional theory (DFT) study

Density functional theory (BLYP, B3LYP, B3P86, B3PW91) with the 6-31+G(d,p), 6-311+G(d,p), and cc-pVTZ basis sets has been used to calculate structural parameters, relative energies, and vibrational spectra of 2-pyrimidinethiol (1) and 2(1H)-pyrimidinethione (2) and their hydrogen-bonded homodimers (C(2) 3, C(2h) [4](double dagger), C(2h) 5), monohydrates, and dihydrates and a heterodimer (6). Several transition state structures proposed for the tautomerization process have also been examined. At the B3PW91/6-311+G(d,p)//B3PW91/6-31+G(d,p) level of theory 2-pyrimidinethiol (1) is predicted to be 3.41 kcal/mol more stable (E(rel)) than 2(1H)-pyrimidinethione (2) in the gas phase and 2 is predicted to be 6.47 kcal/mol more stable than 1 in aqueous medium. An unfavorable planar intramolecular strained four center transition state (TS1) for the tautomerization of 1 and 2 in the gas-phase lies 29.07 kcal/mol higher in energy than 2-pyrimidinethiol (1). The C(2) 2-pyrimidinethiol dimer (3) is 6.84 kcal/mol lower in energy than the C(2) homodimer transition state structure ([11](double dagger)) that connects dimers 3 and 4. Transition state [11](double dagger) provides a facile pathway for tautomerization between 1 and 2 in the gas phase (monomer-dimer promoted tautomerization). The hydrogen bonded 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O structures are predicted to be 1.27 and 1.55 kcal/mol, respectively, higher in energy than 2(1H)-pyrimidinethione- - -H(2)O and 2(1H)-pyrimidinethione- - -2H(2)O. Water promoted tautomerization via cyclic transition states involving one water molecule (TS- - -H(2)O, [12](double dagger)) and two water molecules (TS- - -2H(2)O, [13](double dagger)) lie 11.42 and 11.44 kcal/mol, respectively, higher in energy than 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O. Thus, the hydrated transition states [12](double dagger) and [13](double dagger) are involved in the tautomerism between 1 and 2 in aqueous medium.     

Hexanuclear cobalt carbonyl carbide clusters: the interplay between octahedral and trigonal prismatic structures

The six-vertex cobalt carbonyl clusters [Co6C(CO)n](2-) (n = 12, 13, 14, 15, 16) with an interstitial carbon atom have been studied by density functional theory (DFT). These DFT studies indicate that the experimentally known structure of [Co6C(CO)15](2-) consisting of a Co6 trigonal prism with each of its edges bridged by carbonyl groups is a particularly stable structure lying more than 20 kcal/mol below any other [Co6C(CO)15](2-) structure. Addition of a CO group to this [Co6C(CO)15](2-) structure gives the lowest energy [Co6C(CO)16](2-) structure, also a Co6 trigonal prism with one of the vertical edges bridged by two CO groups and the remaining eight edges each bridged by a single CO group. However, this [Co6C(CO)16](2-) structure is thermodynamically unstable with respect to CO loss reverting to the stable trigonal prismatic [Co6C(CO)15](2-). This suggests that 15 carbonyl groups is the maximum that can be attached to a Co6C skeleton in a stable compound. The lowest energy structure of [Co6C(CO)14](2-) has a highly distorted octahedral Co6 skeleton and is thermodynamically unstable with respect to disproportionation to [Co6C(CO)15](2-) and [Co6C(CO)13](2-). The lowest energy [Co6C(CO)13](2-) structure is very similar to a known stable structure with an octahedral Co6 skeleton. The lowest energy [Co6C(CO)12](2-) structure is a relatively symmetrical D3d structure containing a carbon-centered Co6 puckered hexagon in the chair form.     

The possibility of the decomposition of 2'-deoxyribose moiety of thymidine induced by the low energy electron attachment

To evaluate the possibility of the decomposition of 2-deoxyribose moiety of thymidine induced by low energy electrons (LEE) attachment, the transition states and the energy barriers of the bond breaking processes of the ribose of the nucleoside have been studied theoretically by applying the density functional theory with the double zeta basis sets (DZP++). The energy barriers for the breakage of the C-C bonds (C(1')-C(2'), C(2')-C(3'), C(3')-C(4'), and C(4')-C(5')) of the ribose group of the radical anion of thymidine are found to be high (ca. 42-57 kcal/mol). The total energies of the C-C bond-broken products are significantly higher than that of the radical anion dT(*-). The decomposition of dT(*-) through the C-C bond rupture is unlikely to take place. The rupture of the C(1')-O(4') bond of dT(*-) needs an activation energy as low as 10.4 kcal/mol. However, the reversed reaction (C(1')-O(4') bond formation) needs the activation energy low as 0.3 kcal/mol. Therefore, the intermediate product LM1(C1')-(O4') is unlikely to be stable and the C(1')-O(4') bond-broken is not favored. The activation energy of the C(4')-O(4') bond rupture process amounts to 20.5 kcal/mol. The total energy of the C(4')-O(4') bond broken product is about 6.5 kcal/mol lower than that of the reactant dT(*-). The subsequent N1-glycosidic bond breaking process is found to have a very low energy barrier. Therefore, the LEE-induced base release through the C(4')-O(4') bond rupture might be a possible pathway.     

Effect of geminal substitution at silicon on 1-sila- and 1,3-disilacyclobutanes' strain energies, their 2+2 cycloreversion enthalpies, and Si=C pi-bond energies in silenes.

To evaluate the effect of geminal substitution at silicon on 1-sila- and 1,3-disilacyclobutanes' strain energies, their 2+2 cycloreversion enthalpies, and Si=C pi-bond energies in silenes, an ab initio MO study of silenes, R2Si=CH2 (1), 1-silacyclobutanes, cyclo-R2Si(CH2)3 (2), and 1,3-disilacyclobutanes, cyclo-(R2SiCH2)2 (3), was performed using the level of theory denoted MP4/TZ(d)//MP2/6-31G(d) (TZ means the 6-311G(d) basis set for elements of the second period and hydrogen, and the McLean-Chandler (12s,9p)/[6s,5p](d) basis set for the third period elements). In the series R = H, CH3, SiH3, CH3O, NH2, Cl, F, the growth of the reaction enthalpies and strain energies is proportional to the substituents' electronegativities. 2+2 cycloreversion of 2 is endothermic by 40.6-63.1 kcal/mol, whereas that of 3 is endothermic by 72.7-114.2 kcal/mol. On going from a silicon to a fluorine substituent at the sp2-hybridized silicon atom, the pi-bond energy in 1 weakens by 11.3 kcal/mol, and the Si=C bond length shortens by 0.053 A. The effect of substituents' electronegativities at the double-bonded silicon atom in silenes is formulated as follows: the higher electronegativity, the shorter and the weaker the Si=C pi-bond. The latter is rationalized in terms of more strained geometry resulting from the energetic cost for planarizing the R2SiC moiety. The enthalpies of the ring-opening reaction are 68.0-80.1 kcal/mol (a cleavage of the Si-C bond in 3), 65.0-76.4 kcal/mol (a cleavage of the Si-C bond in 2), and 58.0-64.9 kcal/mol (a cleavage of the C-C bond in 2). The pronounced difference in the enthalpies of 2+2 cycloreversion of 1-sila- and 1,3-disilacyclobutanes is mainly due to the difference in the enthalpies of diradicals' decomposition. The decomposition of diradicals resulting from a cleavage of C-C and Si-C bonds in 2 is exothermic by 24.3-3.3 kcal/mol (apart from the difluoro derivative which is endothermic by 5.1 kcal/mol) and 27.0-13.3 kcal/mol, respectively. The decomposition of a 1,4-diradical resulting from ring opening of 3, apart from the disilyl derivative, is the endothermic process for which the enthalpy varies from 10.6 to 40.4 kcal/mol.     

The electronic structure and energetics of V(+)-benzene half-sandwiches of different multiplicities: Comparative multireference and single-reference theoretical study

Multireference [complete active space self-consistent field (CASSCF) and multiconfigurational quasidegenerate perturbation theory (MCQDPT)] and single-reference ab initio (Moller-Plesset second order perturbation theory (MP2) and coupled clusters with singles, doubles and noniterative triples [CCSD(T)]) and density functional theory (PBE and B3LYP) electronic structure calculations of V(C(6)H(6))(+) half-sandwich in the states of different multiplicities are described and compared. Detailed analyses of the geometries and electronic structures of the all found states are given; adiabatic and diabatic dissociation energies are estimated. The lowest electronic state of V(C(6)H(6))(+) half-sandwich was found to be the quintet (5)B(2) state with a slightly deformed upside-down-boat-shaped benzene ring and d(4) configuration of V atom, followed by a triplet (3)A(2) state lying about 4 kcal/mol above. The lowest singlet state (1)A(1)(d(4)) lies much ( approximately 28 kcal/mol) higher. MCQDPT calculated adiabatic dissociation energy (53.6 kcal/mol) for the lowest (5)B(2)(d(4)) state agrees well with the current 56.4 (54.4) kcal/mol experimental estimate, giving a preference to the lower one. Compared to MCQDPT, B3LYP hybrid exchange-correlation functional provides the best results, while CCSD(T) performs usually worse. Gradient-corrected PBE calculations tend to systematically overestimate metal-benzene binding in the row quintet相似文献   

Theoretical study of the oxygen exchange in uranyl hydroxide. An old riddle solved?

A multistep mechanism for the experimentally observed oxygen exchange [Inorg. Chem. 1999, 38, 1456] of UO2(2+) cations in highly alkaline solutions is suggested and probed computationally. It involves an equilibrium between [UO2(OH)4](2-) and [UO2(OH)5](3-), followed by formation of the stable [UO3(OH)3 x H2O](3-) intermediate that forms from [UO2(OH)5](3-) through intramolecular water elimination. The [UO3(OH)3 x H2O](3-) intermediate facilitates oxygen exchange through proton shuttling, retaining trans-uranyl structures throughout, without formation of the cis-uranyl intermediates proposed earliar. Alternative cis-uranyl pathways have been explored but were found to have activation energies that are too high. Relativistic density functional theory (DFT) has been applied to obtain geometries and vibrational frequencies of the different species (reactants, intermediates, transition states, products) and to calculate reaction paths. Two different relativistic methods were used: a scalar four-component all-electron relativistic method and the zeroeth-order regular approximation. Calculations were conducted for both gas phase and condensed phase, the latter treated using the COSMO continuum model. An activation energy of 12.5 kcal/mol is found in solution for the rate-determining step, the reaction of changing the four-coordinated uranyl hydroxide to the five-coordinated one. This compares favorably to the experimental value of 9.8 +/- 0.7 kcal/mol. Activation energies of 7.8 and 5.1 kcal/mol are found for the hydrogen transfer between equatorial and axial oxygens through a water molecule in [UO3(OH)3 x H2O](3-) in the gas phase and condensed phase, respectively. Contrary to previously proposed mechanisms that resulted in high activation barriers, we find energies that are low enough to facilitate the reaction at room temperature. For the activation energies, two approximate DFT methods, B3LYP and PBE, are compared. The differences in activation energies are only about 1-2 kcal/mol for these methods.     

Si2CN: a stable nitrogen-containing radical with cyclic ground state

The structures and isomerization of Si(2)CN species are explored at density functional theory and ab initio levels. Fourteen minimum isomers are located connected by 23 interconversion transition states. At the coupled-cluster single double (CCSD)(T)/6-311+G(2df)//QCISD/6-311G(d) +zero-point vibrational energies level, the thermodynamically most stable isomer is a four-membered ring form cSiSiCN 1 with Si-C cross bonding. Isomer 1 has very strong C-N multiple bonding characters, formally suggestive of a radical adduct between Si(2) and CN. Such a highly pi-electron localization can effectively stabilize isomer 1 to be the ground state. The second low-lying isomer is a linear form SiCNSi 5 (9.8 kcal/mol above 1) with resonating structure among [Si=C-*N=Si], *[Si=C=N=Si], and [Si=C=N-Si*]* with the former two bearing more weight. The species 1 and 5 have very high kinetic stability stabilized by the barriers of at least 25 kcal/mol. Both isomers should be experimentally or astrophysically observable. In light of the fact that no cyclic nitrogen-containing species have been detected in space, the cyclic species 1 could be a very promising candidate. The calculated results are compared to those of the analogous molecules C(3)N, C(3)P, SiC(2)N, and SiC(2)P. Implications of Si(2)CN in interstellar and N-doped SiC vaporization processes are also discussed.     

Investigation of noncovalent interactions in deprotonated peptides: structural and energetic competition between aggregation and hydration

Noncovalent peptide-peptide and peptide-water interactions in small model systems were examined using an electrospray mass spectrometer equipped with a high-pressure drift cell. The results of these aggregation and hydration experiments were interpreted with the aid of molecular mechanics (MM) and density functional theory (DFT) calculations. The systems investigated include bare deprotonated monomers and dimers [P(1,2)-H](-) and hydrated deprotonated monomers and dimers [P(1,2)-H](-).(H(2)O)(n)() for the peptides dialanine (P = AA) and diglycine (P = GG). Mass spectra indicated that both peptides AA and GG form exclusively dimer ions in the electrospray process. Monomeric ions were generated by high-energy injection of the dimers into the drift cell. Temperature-dependent hydration equilibrium experiments carried out in the drift cell yielded water binding energies ranging from 11.7 (first water molecule) to 7.1 kcal/mol (fourth water) for [AA-H](-) and 11.0 to 7.4 kcal/mol for [GG-H](-). The first water molecule adding to the dimer ions [AA-H](-).(AA) and [GG-H](-).(GG) is bound by 8.4 and 7.5 kcal/mol, respectively. The hydration mass spectra for the monomers and dimers provide a means to compare the ability of water and a neutral peptide to solvate a deprotonated peptide [P-H](-). The data indicate that a similar degree of solvation is achieved by four water molecules, [P-H](-).(H(2)O)(4), or one neutral peptide, [P-H](-).(P). Temperature-dependent kinetics experiments yielded activation energies for dissociation of the dimers [AA-H](-).(AA) and [GG-H](-).(GG) of 34.9 and 32.2 kcal/mol, respectively. MM and DFT calculations carried out for the dialanine system indicated that the dimer binding energy is 24.3 kcal/mol, when the [AA-H](-) and AA products are relaxed to their global minimum structures. However, a value of 38.9 kcal/mol is obtained if [AA-H](-) and AA dissociate but retain the structures of the moieties in the dimer, suggesting the transition state occurs early in the dissociation process. Similar results were found for the diglycine dimer.     

Structure and bonding in Hartwig stretched eta(3)-hydridoborate sigma-complex of niobium(III)

Ab initio calculations at the SCF, MP2, CASSCF, and CASPT2 levels of theory with basis sets using atomic pseudopotentials have been carried out for the stretched eta(3)-hydridoborate sigma-complex of niobium, [Cl2Nb(H2B(OH)2)], in order to investigate the nature and energetics of the interaction between the transition metal and the eta(3)-hydridoborate ligand. The geometry of the complex [Cl2Nb(H2B(OH)2] and its fragments [Cl2Nb](+) and [H2B(OH)2](-) were optimized at SCF and CASSCF levels. These results are consistent with [Cl2Nb(eta(3)-H2B(OH)2)] being a Nb(III) complex in which both hydrogen and boron of the [eta(3)-H2B(OH)2](-) ligand have a bonding interaction with the niobium preserving stretching B-H bond character. The calculated values of DEF (energy required to restore the fragment from the equilibrium structure to the structure it takes in the complex) for [Cl2Nb](+) are 5.35 kcal/mol at SCF, 3.27 kcal/mol at MP2, 4.80 kcal/mol at CASSCF, and 2.82 kcal/mol at CASPT2 and for [H2B(OH)2](-) 21.13 kcal/mol at SCF, 23.85 kcal/mol at MP2, 20.69 kcal/mol at CASSCF, and 23.48 kcal/mol at CASPT2. Values of INT (stabilization energy resulting from the coordination of distorted ligand to the metal fragment) for the complex [Cl2Nb(H2B(OH)2)] are -239.35 kcal/mol at SCF, -260.00 kcal/mol at MP2, -230.76 kcal/mol at CASSCF, and -252.60 kcal/mol at CASPT2. For the complex [(eta(5)-C5H5)2Nb(H2B(OH)2)], calculations at the SCF and MP2 levels were carried out. Values of INT for [(eta(5)-C5H5)2Nb(H2B(OH)2)] are -169.93 kcal/mol at SCF and -210.62 kcal/mol at MP2. The results indicate that the bonding of the [eta(3)-H2B(OH)2](-) ligand with niobium is substantially stable. The electronic structures of [Cl2Nb(H2B(OH)2)], [(eta(5)-C5H5)2Nb(H2B(OH)2)], and its fragments are analyzed in detail as measured by Mulliken charge distributions and orbital populations.     

Fused five-membered rings determine the stability of C60F60

The structure and stability of a set of (CF)60 isomers have been computed at the B3LYP/6-31G(d) density functional theory level. The most stable isomer (6, F4@C60F56) has tube-like structure with four endo C-F bonds and fused five-membered rings at the end of the tube, while the reported most stable cage structure (2, F8@C60F52) with eight endo C-F bonds is higher in energy by 22.6 kcal/mol. This is in contrast to the isolated pentagon rule for the stability of fullerenes. The mean bond dissociation energy of 6 is larger than those of the experimental known C60F36, C60F48, and graphite fluoride. The relative energy per CF unit of 6 to graphite fluoride (CF)n is 3.7 kcal/mol, which is smaller than that of C60 fullerene per carbon to graphite (about 9-10 kcal/mol).     

The mechanism of water oxidation catalysis promoted by [tpyRu(IV)=O]2L3+: a computational study

The resting state of the recently reported water oxidation catalyst [tpyRu(II)-OH(2)](2)L(3+) (tpy = terpyridine; L = bipyridylpyrazolylic anion) ([2,2](3+)) must be activated by a series of proton-coupled oxidations in which four protons and four electrons are removed overall to afford the catalytically competent species [tpyRu(IV)O](2)L(3+) ([4,4](3+)). We have examined all of the plausible redox intermediates utilizing density functional theory coupled to a continuum solvation model. Our calculations reproduce well the first three redox potentials under pH = 1 conditions, and a reasonable correlation between theory and experiment is found for the fourth irreversible redox process that accompanies O(2) generation. The computed oxidation potentials to access [5,4](4+) and [5,5](5+), 1.875 and 2.032 V vs NHE, respectively, exclude the otherwise plausible possibilities of the catalytically active species having a higher oxidation state. [4,4](3+) has an antiferromagnetically coupled ground state in which one ruthenium has two unpaired electrons antiparallel to those of the other ruthenium. As we found in our previous work, two radicaloid terminal oxygen moieties with different spin orientations that are induced by spin polarization from the electron-deficient Ru(IV) centers are found. Two mechanistic scenarios are relevant and interesting for the key O-O bond formation event: intramolecular oxo-oxo coupling and coupling between one terminal oxo and the oxygen atom of the incoming water substrate. The intramolecular oxo-oxo coupling is facile, with a low barrier of 13.9 kcal mol(-1), yielding a peroxo intermediate. The necessary subsequent addition of water in an associative substitution mechanism to cleave one of the Ru-peroxo bonds, however, is found to be impractical at room temperature, with a barrier of DeltaG(double dagger) = 30.9 kcal mol(-1). Thus, while plausible, the intramolecular oxo-oxo coupling is unproductive for generating molecular dioxygen. The intermolecular O-O coupling is associated with a high barrier (DeltaG(double dagger) = 40.2 kcal mol(-1)) and requires the assistance of an additional proton, which lowers the barrier dramatically to 24.5 kcal mol(-1).     

Molecular structure of the octatetranyl anion, C8H-: a computational study

The equilibrium molecular structure of the octatetranyl anion, C8H(-), which has been recently detected in two astronomical environments, is investigated with the aid of both ab initio post-Hartree-Fock and density functional theory (DFT) calculations. The model chemistry adopted in this study was selected after a series of benchmark calculations performed on molecular acetylene for which accurate gas-phase structural data are available. Geometry optimizations performed at the CCSD/6-311+G(2d,p), QCISD/6-311+G(2d,p), and MP4(SDQ)/6-311+G(2d,p) levels of theory yield for C8H(-) an interesting polyyne-type structure that defies the chemical formula displaying a simple alternation of triple and single carbon-carbon bonds, [:C[triple bond]C-C[triple bond]C-C[triple bond]C-C[triple bond]CH](1-). In the optimized geometry of C8H(-), as one proceeds from the naked carbon atom on one side of the chain to the CH unit on the opposite side of the chain, the short (formally triple) carbon-carbon bonds decrease in length from 1.255 to 1.213 A whereas the long (formally single) carbon-carbon bonds increase (albeit only slightly) in length from 1.362 to 1.378 A (CCSD results). In striking contrast, both MP2 and DFT (B3LYP and PBE0) calculations fail in reproducing the pattern of the carbon-carbon bond lengths obtained with the CCSD, QCISD, and MP4 methods. The structures of three shorter n-even chains, C(n)H(-) (n = 2, 4, and 6), along with those of four n-odd compounds (n = 3, 5, 7, and 9) are also investigated at the CCSD/6-311+G(2d,p) level of theory.     

Carbon chains and the (5,5) single-walled nanotube: structure and energetics versus length

Reliable thermochemistry is computed for infinite stretches of pure-carbon materials including acetylenic and cumulenic carbon chains, graphene sheet, and single-walled carbon nanotubes (SWCNTs) by connection to the properties of finite size molecules that grow into the infinitely long systems. Using ab initio G3 theory, the infinite cumulenic chain (:C[double bond]C[double bond]C[double bond]C:) is found to be 1.9+/-0.4 kcal/mol per carbon less stable in free energy at room temperature than the acetylenic chain (.C[triple bond]C-C[triple bond]C.) which is 24.0 kcal/mol less stable than graphite. The difference between carbon-carbon triple, double, and single bond lengths (1.257, 1.279, and 1.333 A, respectively) in infinite chains is evident but much less than with small hydrocarbon molecules. These results are used to evaluate the efficacy of similar calculations with the less rigorous PM3 semiempirical method on the (5,5) SWCNT, which is too large to be studied with high-level ab initio methods. The equilibrium electronic energy change for C(g)-->C[infinite (5,5) SWCNT] is -166.7 kcal/mol, while the corresponding free energy change at room temperature is -153.3 kcal/mol (6.7 kcal/mol less stable than graphite). A threefold alternation (6.866, 6.866, and 6.823 A) in the ring diameter of the equilibrium structure of infinitely long (5,5) SWCNT is apparent, although the stability of this structure over the constant diameter structure is small compared to the zero point energy of the nanotube. In general, different (n,m) SWCNTs have different infinite tube energetics, as well as very different energetic trends that vary significantly with length, diameter, and capping.     

Unexpected direct iron-fluorine bonds in trifluorophosphane iron complexes: an alternative to bridging trifluorophosphane and difluorophosphido groups

The iron trifluorophosphane complexes [Fe(PF(3))(n)] (n=4, 5), [Fe(2)(PF(3))(n)] (n=8, 9), [H(2)Fe(PF(3))(4)], and [Fe(2)(PF(2))(2)(PF(3))(6)] have been studied by density functional theory. The lowest energy structures of [Fe(PF(3))(4)] and [Fe(PF(3))(5)] are a triplet tetrahedron and a singlet trigonal bipyramid, respectively. Both cis and trans octahedral structures were found for [H(2)Fe(PF(3))(4)] with the cis isomer lying lower in energy by approximately 10 kcal mol(-1). The lowest energy structure for [Fe(2)(PF(3))(8)] has two [Fe(PF(3))(4)] units linked only by an iron-iron bond of length 2.505 A consistent with the formal Fe=Fe double bond required to give both iron atoms the favored 18-electron configuration. In the lowest energy structure for [Fe(2)(PF(3))(9)] one of the iron atoms has inserted into a P-F bond of one of the PF(3) ligands to give a structure [(F(3)P)(4)Fe<--PF(2)Fe(F)(PF(3))(4)] with a bridging PF(2) group and a direct Fe-F bond. A bridging PF(3) group is found in a considerably higher energy [Fe(2)(PF(3))(9)] structure at approximately 30 kcal mol(-1) above the global minimum. However, this bridging PF(3) group keeps the two iron atoms too far apart (approximately 4 A) for the direct iron-iron bond required to give the iron atoms the favored 18-electron configuration. The preferred structure for [Fe(2)(PF(2))(2)(PF(3))(6)] has a bridging PF(2) group, as expected. However, this bridging PF(2) group bonds to one of the iron atoms through an P-Fe covalent bond and to the other iron through an F-->Fe dative bond, leaving an uncomplexed phosphorus lone pair.     

Cycloaddition of benzene on Si(100) and its surface conversions

A comprehensive ab initio study of the adsorption of benzene on the silicon(100) surface is presented. Five potential candidates ([2+2] adduct, [4+2] adduct, two tetra-sigma-bonded structures, and one radical-like structure) for the reaction product are examined to determine the lowest energy adsorption configuration. A [4+2] butterfly structure is determined to be the global minimum (-29.0 kcal/mol), although one of the two tetra-sigma-bonded structures (-26.7 kcal/mol) is similar in energy to it. Multireference perturbation theory suggests that the [4+2] addition mechanism of benzene on Si(100) is very similar to the usual Diels-Alder reaction (i.e., small or zero activation barrier), even though benzene adsorption entails the loss of benzene aromaticity during the reaction. On the other hand, the [2+2] cycloaddition mechanism is shown to require a relatively high activation barrier (17.8 kcal/mol), in which the initial step is to form a (relatively strongly bound) van der Waals complex (-8.9 kcal/mol). However, the net activation barrier relative to reactants is only 8.9 kcal/mol. Careful examination of the interconversion reactions among the reaction products indicates that the two tetra-sigma-bonded structures (that are energetically comparable to the [4+2] product) can be derived from the [2+2] adduct with activation barriers of 15.5 and 21.4 kcal/mol. However, unlike the previous theoretical predictions, it is found that the conversion of the [4+2] product to the tetra-sigma-bonded structures entails huge barriers (>37.0 kcal/mol) and is unlikely to occur. This suggests that the [4+2] product is not only thermodynamically the most stable configuration (lowest energy product) but also kinetically very stable (large barriers with respect to the isomerization to other products).     

Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation

Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.     

Pi and sigma-phenylethynyl radicals and their isomers o-, m-, and p-ethynylphenyl: structures, energetics, and electron affinities

Molecular structures, energetics, vibrational frequencies, and electron affinities are predicted for the phenylethynyl radical and its isomers. Electron affinities are computed using density functional theory, -namely, the BHLYP, BLYP, B3LYP, BP86, BPW91, and B3PW91 functionals-, employing the double-zeta plus polarization DZP++ basis set; this level of theory is known to perform well for the computation of electron affinities. Furthermore, ab initio computations employing perturbation theory, coupled cluster with single and double excitations [CCSD], and the inclusion of perturbative triples [CCSD(T)] are performed to determine the relative energies of the isomers. These higher level computations are performed with the correlation consistent family of basis sets cc-pVXZ (X = D, T, Q, 5). Three electronic states are probed for the phenylethynyl radical. In C2v symmetry, the out-of-plane (2B1) radical is predicted to lie about 10 kcal/mol below the in-plane (2B2) radical by DFT methods, which becomes 9.4 kcal/mol with the consideration of the CCSD(T) method. The energy difference between the lowest pi and sigma electronic states of the phenylethynyl radical is also about 10 kcal/mol according to DFT; however, CCSD(T) with the cc-pVQZ basis set shows this energy separation to be just 1.8 kcal/mol. The theoretical electron affinities of the phenylethynyl radical are predicted to be 3.00 eV (B3LYP/DZP++) and 3.03 eV (CCSD(T)/DZP++//MP2/DZP++). The adiabatic electron affinities (EAad) of the three isomers of phenylethynyl, that is, the ortho-, meta-, and para-ethynylphenyl, are predicted to be 1.45, 1.40, and 1.43 eV, respectively. Hence, the phenylethynyl radical binds an electron far more effectively than the three other radicals studied. Thermochemical predictions, such as the bond dissociation energies of the aromatic and ethynyl C-H bonds and the proton affinities of the phenylethynyl and ethynylphenyl anions, are also reported.     

Trifluorosulfane ligand as an analogue of the nitrosyl ligand: highly exothermic fluorine transfer reactions from sulfur to metal in the chemistry of SF3 metal carbonyls of the first row transition metals

The variety of known very stable PF(3) metal derivatives analogous to metal carbonyls suggests the synthesis of SF(3) metal derivatives analogous to metal nitrosyls. However, the only known SF(3) metal complex is the structurally uncharacterized (Et(3)P)(2)Ir(CO)(Cl)(F)(SF(3)) synthesized by Cockman, Ebsworth, and Holloway in 1987 and suggested by electron counting to have a one-electron donor SF(3) group rather than a three-electron donor SF(3) group. In this connection, the possibility of synthesizing SF(3) metal derivatives analogous to metal nitrosyls has been investigated using density functional theory. The [M]SF(3) derivatives with [M] = V(CO)(5), Mn(CO)(4), Co(CO)(3), Ir(CO)(3), (C(5)H(5))Cr(CO)(2), (C(5)H(5))Fe(CO), and (C(5)H(5))Ni analogous to known metal nitrosyl derivatives are all predicted to be thermodynamically disfavored with respect to the corresponding [M](SF(2))(F) derivatives by energies ranging from 19.5 kcal/mol for Mn(SF(3))(CO)(4) to 5.4 kcal/mol for Co(SF(3))(CO)(3). By contrast, the isoelectronic [M]PF(3) derivatives with [M] = Cr(CO)(5), Fe(CO)(4), Ni(CO)(3), (C(5)H(5))Mn(CO)(2), (C(5)H(5))Co(CO), and (C(5)H(5))Cu are all very strongly thermodynamically favored with respect to the corresponding [M](PF(2))(F) derivatives by energies ranging from 64.3 kcal/mol for Cr(PF(3))(CO)(5) to 31.6 kcal/mol for (C(5)H(5))Co(PF(3))(CO). The known six-coordinate (Et(3)P)(2)Ir(CO)(Cl)(F)(SF(3)) is also predicted to be stable relative to the seven-coordinate (Et(3)P)(2)Ir(CO)(Cl)(F)(2)(SF(2)). Most of the metal SF(3) complexes found in this work are singlet structures containing three-electron donor SF(3) ligands with tetrahedral sulfur coordination. However, two examples of triplet spin state metal SF(3) complexes, namely, the lowest energy (C(5)H(5))Fe(SF(3))(CO) structure and a higher energy Co(SF(3))(CO)(3) structure, are found containing one-electron donor SF(3) ligands with pseudo square pyramidal sulfur coordination with a stereochemically active lone electron pair.     

Ring opening of 2,5-didehydrothiophene: structures and rearrangements of C4H2S isomers

Electronic structures and rearrangement pathways of several C4H2S isomers are computationally investigated by methods based on coupled cluster theory and density functional theory. Six singlet C4H2S isomers lie within ca. 30 kcal/mol above butatrienethione (6), the apparent global minimum. Ethynylthioketene (7) lies only 2 kcal/mol higher in energy than cumulene 6. Two open-chain isomers, butadiynylthiol (8) and diethynyl sulfide (9), reside ca. 9 and 24 kcal/mol above 6, respectively. Lying 30 kcal/mol above 6, two cyclic singlet isomers, ethynylthiirene (10) and cyclopropenylidenemethanthione (11), are nearly degenerate in energy. Thiophene-2,5-diyl (12) lies substantially higher in energy than 6 (ca. 45 kcal/mol) and is predicted to rearrange preferentially by C-S bond cleavage, leading to thioketene 7, rather than by C-C bond cleavage, leading to diethynyl sulfide (9; retro-Bergman cyclization). Accurate spectroscopic properties of these C4H2S isomers, as well as an understanding of their rearrangement pathways, should facilitate the detection and characterization of these isomers in the laboratory and the interstellar medium.     

Identification of decomposition reactions for HMDSO organosilicon using quantum chemical calculations

Hexamethyldisiloxane [HMDSO, (CH₃)₃-SiOSi-(CH₃)₃] is an important precursor for SiO₂ formation during flame-based silica material synthesis. As a result, HMDSO reactions in flame have been widely investigated experimentally, and many results have indicated that HMDSO decomposition reactions occur very early in this process. In this paper, quantum chemical calculations are performed to identify the initial decomposition of HMDSO and its subsequent reactions using the density functional theory at the level of B3LYP/6-311+G (d, p). Four reaction pathways—(a) Si O bond dissociation of HMDSO, (b) Si C bond dissociation of HMDSO, (c) dissociation and recombination of Si O and Si C bonds, and (d) elimination of a methane molecule from HMDSO—have been examined and identified. From the results, it is found that the barrier of 84.38 kcal/mol and Si O bond dissociation energy of 21.55 kcal/mol are required for the initial decomposition reaction of HMDSO in the first pathway, but the highest free energy barrier (100.69 kcal/mol) is found in the third reaction pathway. By comparing the free energy barriers and reaction rate constants, it is concluded that the most possible initial decomposition reaction of HMDSO is to eliminate the CH₃ radical by Si C bond dissociation.