Biomedical subjects

Yaoming Xie

Publications and source records attributed to Yaoming Xie.

30 records · Page 2Linked to original sources

PubMed2005

The dichotomy of dimetallocenes: coaxial versus perpendicular dimetal units in sandwich compounds.

Theoretical studies of the dimetallocene (eta5-C5H5)2Zn2 lead to optimized D5h or D5d structures in which the Zn-Zn bond is coaxial with the C5 axes of the two Cp rings, with a Zn-Zn distance of 2.33 A, corresponding to a Zn-Zn single bond. (eta5-C5H5)2Ni2 (singlet state) and (eta5-C5H5)2Cu2 (triplet) have similar structures with a NiNi triple bond (2.06 A) and a Cu=Cu double bond (2.22 A). However, DFT computations on (C5H5)2Ni2 and (C5H5)2Cu2 (both singlet states) lead to a totally different type of optimized structure (Ci symmetry) lying at significantly lower energies, with the metal-metal bonds perpendicular to the C5 axes of the Cp rings.

Journal Article↗

PubMed2005

Perfluoroadamantane and its negative ion.

As a general rule, saturated hydrocarbons are unable to bind an electron, i.e., their electron affinities are negative, but the corresponding perfluorinated molecules can have significant electron affinities, especially in the case of branched and ring systems. Four different density functional theory (DFT) methods in conjunction with double-zeta plus polarization function augmented diffuse function basis sets (DZP++) have been employed to study the equilibrium geometries, electron affinities, and vibrational frequencies of the adamantane (C10H16) and perfluoroadamantane (C10F16) molecules. Three types of neutral-anion separations reported are the adiabatic electron affinity, the vertical electron affinity, and the vertical detachment energy. The adiabatic electron affinity predicted at the DZP++ B3LYP level of theory for adamantane is, as expected, negative (-0.58 eV), while that for perfluoroadamantane is distinctly positive, namely, 1.06 eV (or 1.31 eV after correction for zero-point vibrational energies).

Journal Article↗

PubMed2005

Glycosidic bond cleavage of pyrimidine nucleosides by low-energy electrons: a theoretical rationale.

DNA damage by attachment of low-energy secondary electrons is a very interesting and important mechanism. Electron capture and subsequent base release are thought to be the elementary steps of this mechanism. The process of the N1-glycosidic bond breaking of anion radicals of pyrimidine nucleosides, specifically the 2'-deoxyribothymidine (dT) and 2'-deoxyribocytidine (dC) anions, has been investigated theoretically at the B3LYP/DZP++ level of theory. The release of nucleobases by the attachment of low-energy electrons depends on the formation of a stable anion radical of the nucleoside. The lower bond-breaking activation energy and the higher vertical electron detachment energy for dT enables the heterolytic cleavage of the N1-glycosidic bond. However, with the higher bond-breaking activation energy and the lower vertical electron detachment energy for dC, the release of cytosine might be impractical when the incident electrons have high kinetic energy. Furthermore, the release of cytosine would have a quantum yield much lower than that of dT when the incident electrons have lower kinetic energy. This study also demonstrates the importance of the proton at O5' of 2'-deoxyribose in the base release process. Extending this investigation from dT to dC advances the insight into the mechanism of the N1-glycosidic bond-breaking process. The information from this extensive investigation should be valuable for further experimental studies of cytosine release in irradiated DNA.

DNA Damage↗

PubMed2005

Vibrational frequencies of the homoleptic cobalt carbonyls: Co4(CO)12 and Co6(CO)16.

The homoleptic cobalt carbonyls Co4(CO)12 and Co6(CO)16 are characterized by their equilibrium geometries, thermochemistry, and vibrational frequencies using density functional theory (DFT) methods with the B3LYP, BLYP, and BP86 functionals. The B3LYP predicted CoCo distances are 2.51 and 2.47 A for the C3v and Td structures, respectively, of Co4(CO)12. The global minimum for Co4(CO)12 has C3v symmetry with three bridging and nine terminal carbonyls. The 2.51 and 2.52 A CoCo distances suggest the single bond required for an 18-electron configuration for the metal atoms. This structure is close to an experimentally realized structure. A more symmetrical Co4(CO)12 structure with Td symmetry, analogous to that observed in the valence isoelectronic Ir4(CO)12 molecule, lies approximately 28 kcal/mol higher in energy and exhibits a small imaginary vibrational frequency ( approximately 40i). It has a slightly shorter CoCo distance of 2.47 A. Both Co4(CO)12 structures satisfy the 18-electron rule. The Co6(CO)16 structure has Td symmetry and satisfies the Wade-Mingos rules for an octahedral cluster. The nu(CO) carbonyl frequencies for both Co4(CO)12 and Co6(CO)16 computed with the BP86 functional are closer to the experimental values than those computed with the B3LYP and BLYP functionals. The structure of Co6(CO)16 is not known experimentally, but the BP86 functional predicts 2.56 A (CoCo), 1.77 and 2.02 A (CoC), and 1.66 and 1.20 A (CO) for the bond distances.

Carbon↗

PubMed2004

Hypervalency avoided: simple substituted BrF3 and BrF5 molecules. Structures, thermochemistry, and electron affinities of the bromine hydrogen fluorides HBrF2 and HBrF4.

Five different pure density functional theory (DFT) and hybrid Hartree-Fock/DFT methods have been used to search for the molecular structures, thermochemistry, and electron affinities of the bromine hydrogen fluorides HBrF(n)/HBrF(n)(-) (n = 2, 4). The basis sets used in this work are of double-zeta plus polarization quality in conjunction with s- and p-type diffuse functions, labeled as DZP++. Structures with Br-F and Br-H normal bonds, that is, HBrF(2)/HBrF(2)(-) with C(2v) or C(s) symmetry and HBrF(4)/HBrF(4)(-) with C(4v) or C(s) symmetry, are genuine minima. However, unlike the original BrF(3) and BrF(5) molecules, the global minima for HBrF(n)/HBrF(n)(-) (n = 2, 4) species are predicted to be complexes, some of which contain hydrogen bonds. The demise of the hypervalent structures is due to the availability of favorable dissociation products involving HF, which has a much larger dissociation energy than F(2). Similar reasoning suggests that PF(4)H, SF(3)H, SF(5)H, ClF(2)H, ClF(4)H, AsF(4)H, SeF(3)H, and SeF(5)H will all be hydrogen bond structures incorporating diatomic HF. The most reasonable theoretical values of the adiabatic electron affinities (EA(ad)) are 3.69 (HBrF(2)) and 4.38 eV (HBrF(4)) with the BHLYP method. These electron affinities are comparable to those of the analogous molecules: Br(2)F(n), ClBrF(n), and BrF(n)(+1) systems. The first F-atom dissociation energies for the neutral global minima are 60 (HBrF(2)) and 49 kcal/mol (HBrF(4)) with the B3LYP method. The first H-atom dissociation energies for the same systems are 109 (HBrF(2)) and 116 kcal/mol (HBrF(4)). The large Br-H bond energies are not sufficient to render the hypervalent structures energetically tenable. The dissociation energies for the complexes to their fragments are relatively small.

Journal Article↗

PubMed2004

DNA nucleosides and their radical anions: molecular structures and electron affinities.

The deoxyribonucleosides have been studied to determine the properties of combinations of 2-deoxyribose with each of the isolated DNA bases for both neutral and anionic species. We have used a carefully calibrated theoretical method [Chem. Rev. 2002, 102, 231], employing the B3LYP hybrid Hartree-Fock/DFT functional with the DZP++ basis set. Predictions are made of the geometric parameters, adiabatic electron affinities, charge distributions based on natural population analysis, and decomposition enthalpy for the neutral and anionic forms of the four 2'-deoxyribonucleosides in DNA: 2'-deoxyriboadenosine (dA), 2'-deoxyribocytidine (dC), 2'-deoxyriboguanosine (dG), and 2'-deoxyribothymidine (dT). Geometric changes in the anions show that the glycosidic bond exhibits little change with excess charge for the guanosine but significant shortening for the adenosine and for the pyrimidines. The zero-point corrected adiabatic electron affinities in eV for each of the 2'-deoxyribonucleosides are as follows: 0.06, dA; 0.09, dG; 0.33, dC; and 0.44, dT. These values are uniformly greater than those of the corresponding isolated bases (-0.28, A; -0.07, G; 0.03, C; 0.20, T) and the isolated 2-deoxyribose (-0.38) at the same level of theory. The vertical detachment energies of dT and dC are substantial, 0.72 and 0.94 eV, and these anions should be observable. A high VDE, 0.91 eV, is also found for dA but its anion is unlikely to be stable due to the small AEA of 0.06 eV. The high VDE reflects the fact that the molecular structures of the anions and the corresponding neutral species are quite different. Valence character is displayed for the SOMOs of dA, dC, and dT, while some component of diffuse character is visible in the SOMO of dG. Further analysis of electronic changes upon electron attachment include an examination of the NPA charges, which show that in the neutral 2'-deoxyribonucleosides the sum of NPA charges for every base is the same, -0.28 with the sum of 2-deoxyribose charges being positive, +0.28. In the anions, the trend in charge division varies based on the nature of the excess electron in the anions. Thermodynamically, the overall enthalpy change for the reaction of water with the neutral nucleosides to give bases and ribose is approximately zero. The analogous decomposition is exothermic by 8 to 11 kcal mol-1 for the anions, indicating possible challenges for anionic gas-phase nucleoside exploration in the presence of water.

Anions↗

PubMed2004

The arsenic clusters Asn (n = 1-5) and their anions: structures, thermochemistry, and electron affinities.

The molecular structures, electron affinities, and dissociation energies of the As(n)/As(-) (n) (n = 1-5) species have been examined using six density functional theory (DFT) methods. The basis set used in this work is of double-zeta plus polarization quality with additional diffuse s- and p-type functions, denoted DZP++. These methods have been carefully calibrated (Chem Rev 2002, 102, 231) for the prediction of electron affinities. The geometries are fully optimized with each DFT method independently. Three different types of the neutral-anion energy separations reported in this work are the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). The first dissociation energies D(e)(As(n-1)-As) for the neutral As(n) species, as well as those D(e)(As(-) (n-1)-As) and D(e) (As(n-1)-As(-)) for the anionic As(-) (n) species, have also been reported. The most reliable adiabatic electron affinities, obtained at the DZP++ BLYP level of theory, are 0.90 (As), 0.74 (As(2)), 1.30 (As(3)), 0.49 (As(4)), and 3.03 eV (As(5)), respectively. These EA(ad) values for As, As(2), and As(4) are in good agreement with experiment (average absolute error 0.09 eV), but that for As(3) is a bit smaller than the experimental value (1.45 +/- 0.03 eV). The first dissociation energies for the neutral arsenic clusters predicted by the B3LYP method are 3.93 eV (As(2)), 2.04 eV (As(3)), 3.88 eV (As(4)), and 1.49 eV (As(5)). Compared with the available experimental dissociation energies for the neutral clusters, the theoretical predictions are excellent. Two dissociation limits are possible for the arsenic cluster anions. The atomic arsenic results are 3.91 eV (As(-) (2) --> As(-) + As), 2.46 eV (As(-) (3) --> As(-) (2) + As), 3.14 eV (As(-) (4) --> As(-) (3) + As), and 4.01 eV (As(-) (5) --> As(-) (4) + As). For dissociation to neutral arsenic clusters, the predicted dissociation energies are 2.43 eV (As(-) (3) --> As(2) + As(-)), 3.53 eV (As(-) (4) --> As(3) + As(-)), and 3.67 eV (As(-) (5) --> As(4) + As(-)). For the vibrational frequencies of the As(n) series, the BP86 and B3LYP methods produce good results compared with the limited experiments, so the other predictions with these methods should be reliable.

Journal Article↗

PubMed2003

Binuclear homoleptic manganese carbonyls: Mn2(CO)x (x = 10, 9, 8, 7).

The unsaturated homoleptic manganese carbonyls Mn(2)(CO)(n)() (n = 7, 8, 9) are characterized by their equilibrium geometries, thermochemistry, and vibrational frequencies using methods from density functional theory (DFT). The computed metal-metal distances for global minima range from 3.01 A for the unbridged Mn(2)(CO)(10) with a Mn-Mn single bond to 2.14 A for a monobridged Mn(2)(CO)(7) formulated with a metal-metal quadruple bond. The global minimum for Mn(2)(CO)(9) has a four-electron bridging mu-eta(2)-CO group and a 2.96 A Mn-Mn distance suggestive of the single bond required for 18-electron configurations for both metal atoms. This structure is closely related to an experimentally realized structure for the isolated and structurally characterized stable phosphine complex [R(2)PCH(2)PR(2)](2)Mn(2)(CO)(4)(mu-eta(2)-CO). An unbridged (OC)(4)Mn-Mn(CO)(5) structure for Mn(2)(CO)(9) has only slightly (<6 kcal/mol) higher energy with a somewhat shorter metal-metal distance of 2.77 A. For Mn(2)(CO)(8) the lowest energy structure is a D(2)(d)() unbridged structure with a 2.36 A metal-metal distance suggesting the triple bond required for the favored 18-electron configuration for both metal atoms. However, the unbridged unsymmetrical (CO)(3)Mn-Mn(CO)(5) structure with a metal-metal bond distance of 2.40 A lies only 1 to 3 kcal/mol above this global minimum. The lowest energy structure of Mn(2)(CO)(7) is an unbridged C(s)() structure with a short metal-metal distance of 2.26 A. This is followed energetically by another C(s)() unbridged Mn(2)(CO)(7) structure with a somewhat longer metal-metal distance of 2.38 A.

Crystallography, X-Ray↗

PubMed2003

The radical anions and the electron affinities of perfluorinated benzene, naphthalene and anthracene.

Although benzene and naphthalene do not have electron affinities in the conventional sense, perfluorobenzene and perfluoronaphthalene have nonzero electron affinities. Theoretical methods extensively calibrated with experiment for the prediction of electron affinities (EAs) predict the EAs of perfluorobenzene, perfluoronaphthalene and perfluoroanthracene as 0.69, 1.02 and 1.84 eV, respectively. A rough estimate of 2.39 eV is made for the electron affinity of perfluorotetracene. Thus the perfluoro polycyclic aromatic hydrocarbons (PAHs) are predicted to be effective electron acceptors.

Journal Article↗

PubMed2003

The rule breaking Cr2(CO)10. A 17 electron Cr system or a Cr=Cr double bond?

Density functional theory (DFT) has been used to investigate the conformations and thermochemistry on the singlet and triplet potential energy surfaces (PES) of Cr2(CO)10. The global minimum energy structure for the lowest singlet state of C2h symmetry is consistent with a model of two interacting Cr(CO)5 fragments in which one carbonyl in each fragment acts as an asymmetric four-electron donor bridging carbonyl, with chromium-chromium distances of 2.93 A (B3LYP) or 2.83 A (BP86). Avoiding a Cr...Cr bond by incorporating four-electron donor CO groups in this way allows each chromium atom in singlet Cr(CO)10 to attain the favored 18-electron configuration by using, in a simple picture of the bonding, only the six octahedral sp3d2 hybrids. The dissociation energy to two Cr(CO)5 fragments or to Cr(CO)6 + Cr(CO)4 fragments is predicted to be 10 kcal mol(-1). The lowest triplet state of Cr2(CO)10 is predicted to lie approximately 10 kcal mol(-1) above the singlet global minimum. In the case of triplet Cr2(CO)10 the lowest energy minima were found to be of C2 and C2h symmetry, with similar energies. The chromium-chromium distances in triplet Cr2(CO)10 were found to be shorter than those in the corresponding singlet structures, namely 2.81 (B3LYP) or 2.68 A (BP86) suggesting a sigma + 2(1/2) pi Cr=Cr double bond similar to the O=O bond in O2 or the Fe=Fe bond in the experimentally observed triplet state (Me5C5)2Fe2(mu-CO)3.

Journal Article↗

PubMed2002

Molecules for materials: structures, thermochemistry, and electron affinities of the digermanium fluorides Ge2Fn/Ge2Fn- (n = 1-6): a wealth of unusual structures.

A systematic investigation of Ge2Fn/Ge2Fn- systems was carried out with five density functional theory (DFT) methods in conjunction with DZP++ basis sets. For each compound various structures, including minima, transition states and other energetically low lying stationary points, were optimized. The geometries and relative energies are discussed and compared. Adiabatic electron affinities, vertical electron affinities and anion vertical detachment energies are reported. Three types of dissociation energies pertaining to the global minima for each compound are reported. The theoretical predictions are in good agreement with the limited available experimental results. Many unusual structural features are predicted for these systems. Neutral Ge2F is predicted to have a bridged C2v structure, while its anion is very floppy, with the bridged structure very slightly favoured. The Ge2F2 molecule is predicted to have the butterfly structure known from experiment for Si2H2, while the Ge2F3- ion has a trans-bent structure. Ge2F3 is predicted to have an unprecedented FGe-F-GeF structure with no Ge-Ge bond, while its anion has a somewhat more conventional monobridged structure, analogous to that of the nonclassical vinyl cation. Neutral Ge2F4 has a dibridged structure of C2h symmetry, while its anion has a trans-bent structure with a very long Ge-Ge bond. The Ge2F5 molecule is doubly bridged and has no Ge-Ge bond, while the anion is of the type F2Ge-F-GeF2, again with no Ge-Ge bond. Ge2F6 has the anticipated ethane structure, as does its anion, but with a very long Ge-Ge bond. The adiabatic electron affinities (EAad) are predicted to be 2.12 (Ge2F), 2.03 (Ge2F2), 2.02 (Ge2F3), 1.64 (Ge2F4), 4.57 (Ge2F5), and 2.66 eV (Ge2F6), respectively, by the BHLYP method, which is regarded as the best method in the present paper for predicting EAs. Comparisons with the analogous C2Fn and Si2Fn systems reveals some interesting trends and differences. For example, while C2F6 will not capture an electron, Si2F6 is predicted to have small electron affinity (0.73 eV), while that of Ge2F6 is substantial. The same trend to larger EAs on going down the Periodic Table is seen for the X2F5 systems, with 1.77 (C2F5), 2.68 (Si2F5), and 4.57 eV (Ge2F5). However, the EAs do not follow a monotonic trend for the X2F, X2F3 and X2F4 systems with respect to the series X = C, Si, Ge.

Journal Article↗

PubMed2002

Molecules for materials: germanium hydride neutrals and anions. Molecular structures, electron affinities, and thermochemistry of GeHn/GeHn- (n = 0-4) and Ge2Hn/Ge2Hn(-) (n = 0-6).

The GeH(n) (n = 0-4) and Ge(2)H(n) (n = 0-6) systems have been studied systematically by five different density functional methods. The basis sets employed are of double-zeta plus polarization quality with additional s- and p-type diffuse functions, labeled DZP++. For each compound plausible energetically low-lying structures were optimized. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chemical Reviews 102, 231, 2002). The geometries predicted in this work include yet unknown anionic species, such as Ge(2)H(-), Ge(2)H(2)(-), Ge(2)H(3)(-), Ge(2)H(4)(-), and Ge(2)H(5)(-). In general, the BHLYP method predicts the geometries closest to the few available experimental structures. A number of structures rather different from the analogous well-characterized hydrocarbon radicals and anions are predicted. For example, a vinylidene-like GeGeH(2) (-) structure is the global minimum of Ge(2)H(2) (-). For neutral Ge(2)H(4), a methylcarbene-like HGë-GeH(3) is neally degenerate with the trans-bent H(2)Ge=GeH(2) structure. For the Ge(2)H(4) (-) anion, the methylcarbene-like system is the global minimum. The three different neutral-anion energy differences reported in this research are: the adiabatic electron affinity (EA(ad)), the vertical electron affinity (EA(vert)), and the vertical detachment energy (VDE). For this family of molecules the B3LYP method appears to predict the most reliable electron affinities. The adiabatic electron affinities after the ZPVE correction are predicted to be 2.02 (Ge(2)), 2.05 (Ge(2)H), 1.25 (Ge(2)H(2)), 2.09 (Ge(2)H(3)), 1.71 (Ge(2)H(4)), 2.17 (Ge(2)H(5)), and -0.02 (Ge(2)H(6)) eV. We also reported the dissociation energies for the GeH(n) (n = 1-4) and Ge(2)H(n) (n = 1-6) systems, as well as those for their anionic counterparts. Our theoretical predictions provide strong motivation for the further experimental study of these important germanium hydrides.

Journal Article↗