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Yaoming Xie

Publications and source records attributed to Yaoming Xie.

At least 19 recordsLinked to original sources
PubMed2006

Manganese carbonyl nitrosyls: comparison with isoelectronic iron carbonyl derivatives.

The manganese carbonyl nitrosyls Mn(NO)(CO)4, Mn2(NO)2(CO)n (n = 7, 6, 5, 4), and Mn3(NO)3(CO)9 have been studied by density functional theory (DFT) using the B3LYP and BP86 methods for comparison of their predicted structures with those of isoelectronic iron carbonyl derivatives. DFT predicts a trigonal bipyramidal structure for Mn(NO)(CO)4 with an equatorial NO group very close to the experimental structure. The predicted lowest energy structure for Mn2(NO)2(CO)7 has two bridging NO groups in contrast to the known structure of the isoelectronic Fe2(CO)9, which has three bridging CO groups. The structures for the unsaturated binuclear Mn2(NO)2(CO)n (n = 6, 5, 4) derivatives are similar to those of the corresponding binuclear iron carbonyls Fe2(CO)n+2 derivatives but always with a preference of bridging NO groups over bridging CO groups. The trinuclear Mn3(NO)3(CO)9 is predicted to have a structure analogous to the known structure for Fe3(CO)12 but with two bridging NO groups rather than two bridging CO groups across one of the metal-metal edges of the M3 triangle. The dark red solid photolysis product of Mn(NO)(CO)4 characterized by its nu(CO) and nu(NO) frequencies approximately 45 years ago is suggested by these DFT studies not to be the originally assumed Mn2(NO)2(CO)7 analogous to Fe2(CO)9. Instead, this photolysis product appears to be Mn2(NO)2(CO)5 with a Mn(triple bond)Mn formal triple bond analogous to (eta5-C5H5)2V2(CO)5 obtained from the photolysis of (eta5-C5H5)V(CO)4.

Journal Article↗
PubMed2006

Successive attachment of electrons to protonated Guanine: (G+H)* radicals and (G+H)- anions.

The structures, energetics, and vibrational frequencies of nine hydrogenated 9H-keto-guanine radicals (G+H)(*) and closed-shell anions (G+H)(-) are predicted using the carefully calibrated (Chem. Rev. 2002, 102, 231) B3LYP density functional method in conjunction with a DZP++ basis set. These radical and anionic species come from consecutive electron attachment to the corresponding protonated (G+H)(+) cations in low pH environments. The (G+H)(+) cations are studied using the same level of theory. The proton affinity (PA) of guanine computed in this research (228.1 kcal/mol) is within 0.7 kcal/mol of the latest experiment value. The radicals range over 41 kcal/mol in relative energy, with radical r1, in which H is attached at the C8 site of guanine, having the lowest energy. The lowest energy anion is a2, derived by hydride ion attachment at the C2 site of guanine. No stable N2-site hydride should exist in the gas phase. Structure a9 was predicted to be dissociative in this research. The theoretical adiabatic electron affinities (AEA), vertical electron affinities, and vertical detachment energies were computed, with AEAs ranging from 0.07 to 3.12 eV for the nine radicals.

Anions↗
PubMed2006

Understanding electron attachment to the DNA double helix: the thymidine monophosphate-adenine pair in the gas phase and aqueous solution.

Electron attachment to the 2'-deoxythymidine-5'-monophosphate-adenine pairs (5'-dTMPH-A and 5'-dTMP(-)-A) has been investigated at a carefully calibrated level of theory (B3LYP/DZP++) to investigate the electron-accepting properties of thymine (T) in the DNA double helix under physiological conditions. All molecular structures have been fully optimized in vacuo and in solution. The adiabatic electron affinity of 5'-dTMPH-A in the gas phase has been predicted to be 0.67 eV. Solvent effects greatly increase the electron capture ability of 5'-dTMPH-A. In fact, the adiabatic electron affinity increases to 2.04 eV with solvation. The influence of the solvent environment on the electron-attracting properties of 5'-dTMPH-A arises not only from the stabilization of the corresponding radical anion through charge-dipole interactions, but also by changing the distribution of the unpaired electron in the molecular system. The unpaired electron is covalently bound even during vertical attachment, due to the solvent effects. Solvent effects also weaken the pairing interaction in the thymidine monophosphate-adenine complexes. The phosphate deprotonation is found to have a relatively minor influence on the capture of electrons by the 5'-dTMPH-A species in aqueous solution. The electron distributions, natural population analysis, and geometrical features of the models examined illustrate that the influence of the phosphate deprotonation is limited to the phosphate moiety in aqueous solution. Therefore, it is reasonable to expect that electron attachment to nucleotides will be independent of monovalent counterions in the vicinity of the phosphate group in aqueous solution.

Adenine↗
PubMed2006

Remarkable aspects of unsaturation in trinuclear metal carbonyl clusters: the triiron species Fe3(CO)n (n = 12, 11, 10, 9).

The trinuclear iron carbonyls Fe(3)(CO)(n) (n = 12, 11, 10, 9) have been studied by density functional theory using the B3LYP and BP86 functionals. The experimentally known C(2)(v) isomer of Fe(3)(CO)(12), namely Fe(3)(CO)(10)(mu-CO)(2), is found to be the global minimum below the unbridged D(3)(h) isomer analogous to the known structures for Ru(3)(CO)(12) and Os(3)(CO)(12). The lowest-energy isomer found for Fe(3)(CO)(11) is Fe(3)(CO)(9)(mu(3)-CO)(2) with iron-iron distances in the Fe(3) triangle, suggesting the one double bond (2.460 A by B3LYP and 2.450 A by BP86) and two single bonds (2.623 A by B3LYP and 2.604 A by BP86) required to give each Fe atom the favored 18-electron configuration. Two different higher-energy dibridged structures Fe(3)(CO)(9)(mu(2)-CO)(2) are also found for Fe(3)(CO)(11). The lowest-energy isomer found for Fe(3)(CO)(10) is Fe(3)(CO)(9)(mu(3)-CO) with equivalent iron-iron distances in the Fe(3) ring (2.47 A by B3LYP or BP86). The lowest-energy isomer found for Fe(3)(CO)(9) is Fe(3)(CO)(6)(mu-CO)(3) with distances in the Fe(3) triangle possibly suggesting one single bond (2.618 A by B3LYP and 2.601 A by BP86), one weak double bond (2.491 A by B3LYP and 2.473 A by BP86), and one weak triple bond (2.368 A by B3LYP and 2.343 A by BP86). A higher-lying isomer of Fe(3)(CO)(9), i.e., Fe(3)(CO)(8)(mu-CO), at approximately 21 kcal/mol above the global minimum, has iron-iron distances strongly suggesting two single bonds (2.6 to 2.7 A) and one quadruple bond (2.068 A by B3LYP and 2.103 A by BP86). Wiberg Bond Indices are also helpful in evaluating the iron-iron bond orders.

Journal Article↗
PubMed2006

Molecular oxygen dianions trapped in lithium cluster cages.

In an important recent report, Coles and Hitchcock (Chem. Commun. 2005, 3165) have synthesized a unique compound of the form Li9O2(hpp)7, with an O2 unit encapsulated in the Li cluster. The group hpp is the bicyclic guanidinate 1,3,4,6,7,8-hexahydropyrimido[1,2-a]pyrimidinate. Coles and Hitchcock raise the interesting possibility that the trapped species is the O2 dianion. We have theoretically investigated (with full geometry optimization) the structural, vibrational, and electronic properties of this fascinating system with 165 atoms. Every indication supports the qualitative conclusion that this system is best represented as an O2 dianion embedded in a Li cluster. Several smaller model systems, including replacement of the hpp ligands by Cl atoms, are also examined and provide some interesting comparisons.

Journal Article↗
PubMed2006

Binuclear cyclopentadienylmetal nitrosyls of iron, cobalt, and nickel: comparison with related carbonyl derivatives.

The binuclear cyclopentadienylmetal nitrosyls and carbonyls Cp2M2(AO)n (A = N, M = Fe, Co, Ni; A = C, M = Ni; n = 2, 1) are studied by density functional theory using the B3LYP and BP86 functionals. In general, structures with bridging AO ligands are energetically preferred over those with terminal AO ligands. Thus, the global minima for Cp2M2(AO)2 are all found to have closely related axial dimetallocene structures with two symmetrically bridging AO ligands but variable planarity of the central M(mu-AO)2M units. Similarly, the single AO ligands in the global minima for Cp2M2(AO) are found to bridge symmetrically the pair of metal atoms. However, structures with terminal AO groups and a single bridging Cp ligand are also found at accessible energies for CpM2(NO)(mu-Cp) (M = Fe and Co) and CpNi2(CO)(mu-Cp). The metal-metal bond distances in Cp2M2(AO)n derivatives correlate reasonably well with the requirements of the 18-electron rule. In this connection, the unusual dimer Cp2Ni2(mu-NO)2 has a Ni-Ni bond distance suggestive of a single bond and geometry suggesting one one-electron donor bridging NO group and one three-electron donor bridging NO group. However, dissociation of Cp2Ni2(mu-NO)2 into the well-known stable monomer CpNiNO is highly favored energetically.

Journal Article↗
PubMed2006

Molecular mechanics (MM4) study of fluorinated hydrocarbons.

A molecular mechanics study of small saturated hydrocarbons (up to C-6) substituted by up to six fluorines has been carried out with the MM4 force field. A parameter set has been developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia, and vibrational frequencies for these compounds. The results are mostly in fair to good agreement with experiment and ab initio calculations. The high electronegativity of fluorine leads to serious geometric consequences in these compounds, but these consequences can be dealt with adequately by suitable cross-terms in the force constant matrix, and by recognizing that some of the reference bond lengths and angles (l(0), theta(0)) and the corresponding stretching and bending constant parameters (k(s), k(theta)) that are usually thought of as constants must in fact be treated as functions of the electronegativity of the substituents. Additionally, the heavy mass of the fluorine (relative to the mass of hydrogen in alkanes) leads to large values for other cross-terms that were found to be unimportant in hydrocarbons. Conformational equilibria for polyfluorinated compounds are affected by the delta-two effect well-known in carbohydrates. A few larger fluorinated and polyfluorinated alkanes, including perfluoropropane, perfluorobutane, and Teflon, have also been studied.

Journal Article↗
PubMed2006

Is the uniform electron gas limit important for small Ag clusters? Assessment of different density functionals for Ag(n) (n < or = 4).

Twenty-three density functional theory (DFT) methods, including the second- and the third-generation functionals, are tested in conjunction with two basis sets (LANL2DZ and SDD) for studying the properties of neutral and ionic silver clusters. We find that DFT methods incorporating the uniform electron gas limit in the correlation functional, namely, those with Perdew's correlation functionals (PW91, PBE, P86, and TPSS), Becke's B95, and the Van Voorhis-Scuseria functional VSXC, generally perform better than the other group of functionals, e.g., those incorporating the LYP correlation functional and variations of the B97 functional. Strikingly, these two groups of functionals can produce qualitatively different results for the Ag3 and Ag4 clusters. The energetic properties and vibrational frequencies of Ag(n) are also evaluated by the different functionals. The present study shows that the choice of DFT methods for heavy metals may be critical. It is found that the exact-exchange-incorporated PBE functional (PBE1PBE) is among the best for predicting the range of properties.

Journal Article↗
PubMed2006

Unsaturation in binuclear cyclopentadienyliron carbonyls.

The binuclear cyclopentadienyliron carbonyls Cp2Fe2(CO)n (n = 4, 3, 2, 1; Cp = eta(5)-C5H5) have been studied by density functional theory (DFT) using the B3LYP and BP86 methods. The trans- and cis-Cp2Fe2(CO)2(mu-CO)2 isomers of Cp2Fe2(CO)4 known experimentally are predicted by DFT methods to be genuine minima with no significant imaginary vibrational frequencies. The energies of these two Cp2Fe2(CO)2(mu-CO)2 structures are very similar, consistent with the experimental observation of an equilibrium between these isomers in solution. An intermediate between the interconversion of the trans- and cis-Cp2Fe2(CO)2(mu-CO)2 dibridged isomers of Cp2Fe2(CO)4 can be the trans unbridged isomer of Cp2Fe2(CO)4 calculated to be 2.3 kcal/mol (B3LYP) or 9.1 kcal/mol (BP86) above the global minimum trans-Cp2Fe2(CO)2(mu-CO)2. For the unsaturated Cp2Fe2(CO)3, the known triplet isomer Cp2Fe2(mu-CO)3 with an Fe=Fe double bond similar to the O=O double bond in O2 is found to be the global minimum. The lowest-energy structure for the even more unsaturated Cp2Fe2(CO)2 is a dibridged structure Cp2Fe2(mu-CO)2, with a short Fe-Fe distance suggestive of the Fe[triple bond]Fe triple bond required to give both Fe atoms the favored 18-electron configuration. Singlet and triplet unbridged structures for Cp2Fe2(CO)2 were also found but at energies considerably higher (20-50 kcal/mol) than that of the global minimum Cp2Fe2(mu-CO)2. The lowest-energy structure for Cp2Fe2(CO) is the triplet unsymmetrically bridged structure Cp2Fe2(mu-CO), with a short Fe-Fe distance (approximately 2.1 A) suggestive of the sigma + 2pi + (2/2)delta Fe[quadruple bond]Fe quadruple bond required to give both Fe atoms the favored 18-electron rare gas configuration.

Journal Article↗
PubMed2006

Near 0 eV electrons attach to nucleotides.

To elucidate the mechanism of the nascent stage of DNA strand breakage by low-energy electrons, theoretical investigations of electron attachment to nucleotides have been performed by the reliably calibrated B3LYP/DZP++ approach (Chem. Rev. 2002, 102, 231). The 2'-deoxycytidine-3'-monophosphate (3'-dCMPH) and its phosphate-deprotonated anion (3'-dCMP(-)) have been selected herein as models. This investigation reveals that 3'-dCMPH is able to capture near 0 eV electrons to form a radical anion which has a lower energy than the corresponding neutral species in both the gas phase and aqueous solution. The excess electron density is primarily located on the base of the nucleotide radical anion. The electron detachment energy of this pyrimidine-based radical anion is high enough that subsequent phosphate-sugar C-O sigma bond breaking or glycosidic bond cleavage is feasible. Although the phosphate-centered radical anion of 3'-dCMPH is not stable in the gas phase, it may be stable in aqueous solution. However, an incident electron with kinetic energy less than 4 eV might not be able to effectively produce the phosphate-centered radical anion either in solution or in the gas phase. This research also suggests that the electron affinity of the nucleotides is independent of the counterion in aqueous solution.

DNA↗
PubMed2006

Remarkable electron accepting properties of the simplest benzenoid cyanocarbons: hexacyanobenzene, octacyanonaphthalene and decacyanoanthracene.

The optimised structures, electron affinities, and vibrational frequencies of the simplest benzenoid cyanocarbons, namely hexacyanobenzene C6(CN)6, octacyanonaphthalene C10(CN)8, and decacyanoanthracene C14(CN)10, have been studied using carefully calibrated density functional methods (Chem. Rev., 2002, 102, 231-282); the predicted adiabatic electron affinities are 3.53 eV for C6(CN)6, 4.35 eV for C10(CN)8 and 5.02 eV for C14(CN)10, which are significantly larger than those of the analogous benzenoid fluorocarbons as well as tetracyanoethane and tetracyanoquinodimethane.

Journal Article↗
PubMed2005

13C NMR relaxation study of molecular motions in tetraphenyltin and tetra(p-tolyl)tin in solution.

The Woessner approach is applied to the 13C relaxation data for tetraphenyltin (1) and tetra(p-tolyl)tin (2) in CDCl3 solution over the temperature range 5-42 degrees C to obtain correlation times for rotational motions and hence the activation barriers. Quantum mechanical computations were carried out to obtain the rotational energy barriers for comparison. For 2 the relaxation data indicate (1) slower ring rotation than in 1, (2) highly hindered internal rotation of the methyl group. IR and chemical shift data support the hypothesis of hyperconjugation of the methyl correlated with interaction between the pi-electrons and the 5d orbitals of tin in the (p-tolyl)Sn moiety to account for the hindrances to the rotations of the ring and the methyl. The activation barrier for the tolyl group rotation is found to be much higher than that for the phenyl rotation. However, the Woessner approach yields an anomalously high barrier for the methyl rotation. An explanation based on correlated rotations of the tolyl ring and the methyl is offered.

Journal Article↗
PubMed2005

Nonacarbonyldivanadium: alternatives to metal-metal quadruple bonding.

The first structural characterization of the highly unsaturated nonacarbonyldivanadium V(2)(CO)(9) is reported using density functional theory (DFT) with the B3LYP and BP86 functionals. A complicated collection of minima with rather closely spaced energies was found. However, none of these many V(2)(CO)(9) isomers was found to have a sufficiently short vanadium-vanadium distance for the VV quadruple bond required to give both metal atoms the favored 18-electron configuration. Triplet structures for V(2)(CO)(9) were found to be competitive in energy with related singlet structures. Thus, the two lowest-energy isomers of V(2)(CO)(9) are triplets. The four lowest-energy isomers of V(2)(CO)(9) all have three very unsymmetrical bridging CO groups (typically "short" and "long" M-CO distances differing by 0.4-0.5 A) rather than the symmetrical bridging CO groups found experimentally in Fe(2)(CO)(9) and predicted for M(2)(CO)(9) (M = Cr and Mn) from earlier studies. The VV distances in each of these four isomers suggest a metal-metal triple bond. Next higher in energy for V(2)(CO)(9) are three structures with single four-electron donor bridging CO groups identified by their computed nu(CO) frequencies and V-O distances. The V-V distances in these three isomers suggest metal-metal single bonds. This study of V(2)(CO)(9) supports the following general points: (1) Metal-metal bonds of an order higher than three are not favorable in metal carbonyl chemistry. (2) The 18-electron rule for metal carbonyls begins to break down when the metal atom, i.e., vanadium in this case, has only five valence electrons.

Journal Article↗
PubMed2005

The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage.

The 2'-deoxyadenosine-5'-phosphate (5'-dAMP) anion and its related radicals have been studied by reliably calibrated theoretical approaches. This study reveals important physical characteristics of 5'-dAMP radical related processes. One-electron oxidation of the 5'-dAMP anion is found on both the phosphoryl group and the adenine base with electron detachment energies close to that of phosphate. Partial removal of electron density from the adenine fragment leads to an extended pi system which includes the amine group of the adenine. Although the radical-centered carbon increases the extent of bonding with its adjacent atoms, it usually weakens the chemical bonds between the atoms at the alpha- and beta-positions. This tendency should be important in predicting the reactivity of the sugar-based radicals. The overall stability sequence of the H-abstracted 5'-dAMP anionic radicals is consistent with the analogous results for the H-abstracted neutral radicals of the adenosine nucleoside: aliphatic radicals > aromatic radicals. The negatively charged phosphoryl group attached to atom C(5)' of the ribose does not change this energetic sequence. All the H-abstraction produced 5'-dAMP radical anions are distonic radical anions. Studies have shown that the charge-radical-separating feature of the distonic radical anions is biologically relevant. This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals.

Anions↗
PubMed2005

On the chemistry of Zn-Zn bonds, RZn-ZnR (R = [{(2,6-Pri2C6H3)N(Me)C}2CH]): synthesis, structure, and computations.

Potassium reduction of RZn(mu-I)2Li(OEt2)2 (R = [{(2,6-Pri2C6H3)N(Me)C}2CH]) affords the second compound with a Zn-Zn bond, RZn-ZnR. The air- and moisture-sensitive title compound was characterized by 1H NMR, elemental analyses, and single-crystal X-ray diffraction. The Zn-Zn bond was determined to be 2.3586(7) A; this value is only about 0.05 A longer than the Zn-Zn bond reported for Cp*Zn-ZnCp* (Cp* = C5Me5), the first reported compound with a Zn-Zn bond. In addition, density functional theory (DFT) computations on related model RZn-ZnR compounds provide insight into the intriguing Zn-Zn bond.

Journal Article↗
PubMed2005

Binuclear cyclopentadienylcobalt carbonyls: comparison with binuclear iron carbonyls.

The binuclear cyclopentadienylcobalt carbonyls Cp2Co2(CO)n (n = 3, 2, 1; Cp = eta5-C5H5) are studied by density functional theory using the B3LYP and BP86 functionals. The experimentally known monobridged isomer Cp2Co2(CO)2(mu-CO) and the tribridged isomer Cp2Co2(mu-CO)3 of Cp2Co2(CO)3 with formal Co-Co single bonds are found to be similar in energy, with the precise relative energies of the two isomers depending on the functional chosen. For Cp2Co2(CO)2, the experimentally known coaxial isomer Cp2Co2(mu-CO)2 with two bridging CO groups and a formal Co=Co double bond (2.360 angstroms by B3LYP or 2.346 angstroms by BP86) is found to lie 38.2 (B3LYP) or 34.9 kcal/mol (BP86) below a perpendicular isomer perpendicular-Cp2Co2(CO)2. Similarly, for Cp2Co2(CO), the coaxial isomer Cp2Co2(mu-CO) with one bridging CO group and a formal CoCo triple bond (2.021 angstroms by B3LYP or 2.050 angstroms by BP86) is found to lie 9.36 (B3LYP) or 9.62 kcal/mol (BP86) below the corresponding perpendicular isomer perpendicular-Cp2Co2(CO). This coaxial isomer Cp2Co2(mu-CO) is a possible intermediate in the known pyrolysis of the trimer (eta5-C5H5)3Co3(mu-CO)3 to give the tetranuclear complex (eta5-C5H5)4Co4(mu3-CO)2. These optimized Cp2Co2(CO)n (n = 3, 2, 1) structures can be compared with the corresponding Fe2(CO)6+n structures since the CpCo and Fe(CO)3 groups are isolobal. In general, the metal-metal bonds are 0.09-0.22 angstroms shorter for the Cp2Co2(CO)n (n = 3, 2, 1) complexes than for the corresponding Fe2(CO)6+n complexes. For Fe2(CO)9, the experimentally well-known Fe2(CO)6(mu-CO)3 isomer is shown to be very close in energy to the unknown Fe2(CO)8(mu-CO) isomer, with the precise relative energies depending on the basis set used.

Carbon↗
PubMed2005

Structural and energetic characterization of a DNA nucleoside pair and its anion: deoxyriboadenosine (dA)-deoxyribothymidine (dT).

The geometries of the DNA nucleoside pairs between 2'-deoxyriboadenosine (dA) and 2'-deoxyribothymidine (dT) and its anion (dAdT-) were fully optimized using carefully calibrated density functional methods. The addition of an electron to dAdT results in remarkable changes to the two hydrogen bonding distances, the H...O distance decreasing by 0.303 angstroms and the N...H distance increasing by 0.229 angstroms. The electron affinity of the dAdT pair was studied to reveal the correct trends of adiabatic electron affinity (EA(ad)) under the influence of the additional components to the individual bases. The consequence of negative charge in terms of structural variations, energetic changes, and charge distribution were explored. The EA(ad) of dAdT is predicted to be positive (0.60 eV), and it exhibits a substantial increase compared with those of the corresponding bases A and T and the nucleic acid base pair AT. The effects of pairing and the addition of the sugar moiety on the EA(ad) are well described as the summation of the individual influences. The influence of the pairing on the EA is comparable to that of the addition of 2-deoxyribose. The excess charge is mainly located on the thyminyl moiety in the anionic dAdT pair. The positive vertical electron affinity (VEA = 0.20 eV) for dAdT suggests that it is able to form a stable anion through electron attachment. A large vertical detachment energy (VDE = 1.14 eV) has been determined for the anionic dAdT nucleoside pair. Therefore, one may expect that the stable anionic dAdT nucleoside pair should be able to undergo the subsequent glycosidic bond cleavage process.

Adenosine↗