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Henry F Schaefer

Publications and source records attributed to Henry F Schaefer.

At least 55 records · Page 3Linked to original sources
PubMed2005

The peculiar trend of cyclic perfluoroalkane electron affinities with increasing ring size.

The adiabatic electron affinities (AEAs), vertical electron affinities (VEAs), and vertical detachment energies (VDEs) of cyclic perfluoroalkanes, c-C(n)F(2n) (n = 3-7), and their monotrifluoromethyl derivatives were computed using various pure and hybrid density functionals with DZP++ (polarization and diffuse function augmented double-zeta) basis sets. The theoretical AEA of c-C(4)F(8) at KMLYP/DZP++ is 0.70 eV, which exhibits satisfactory agreement with the 0.63 +/- 0.05 eV experimental value. The nonzero-point-corrected AEA of c-C(4)F(8) is predicted to be 0.41 eV at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ level of theory, which shows a slight deviation of 0.11 eV from the KMLYP estimated value of 0.52 eV for the same. With the zero-point correction from the MP2/6-311G(d) [Gallup, G. A. Chem. Phys. Lett. 2004, 399, 206] level of theory combined with the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ result, the most reliable estimate of AEA of c-C(4)F(8) is 0.60 eV. c-C(3)F(6)(-), c-C(4)F(8)(-), and c-C(5)F(10)(-) are unusual in preferring planar to near planar ring structures. The ZPE-corrected AEAs of c-C(n)F(2n) increase from n = 3 (0.24 eV) to n = 5 (0.77 eV), but then dramatically fall off to 0.40 eV for both n = 6 and n = 7. All of the other functionals predict the same trend. This is due to a change in the structural preference: C(s)() c-C(6)F(12)(-) and C(1) c-C(7)F(14)(-) are predicted to favor nonplanar rings, each with an exceptionally long C-F bond. (There also is a second, higher energy D3d minimum for C(6)F(12)(-).) The SOMOs as well as the spin density plots of the c-PFA radical anions reveal that the "extra" electron is largely localized on the unique F atoms in the larger n = 6 and n = 7 rings but is delocalized in the multiatom SOMOs of the three- to five-membered ring radical anions. The computed AEAs are much larger than the corresponding VEAs; the latter are not consistent with different functionals. The AEAs are substantially larger when a c-C(n)()F(2)(n)() fluorine is replaced by a -CF(3) group. This behavior is general; PFAs with tertiary C-F bonds have large AEAs. The VDEs for all the anions are substantial, ranging from 1.89 to 3.64 eV at the KMLYP/DZP++ level.

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

Homonuclear transition-metal trimers.

Density-functional theory has been used to determine the ground-state geometries and electronic states for homonuclear transition-metal trimers constrained to equilateral triangle geometries. This represents the first application of consistent theoretical methods to all of the ten 3d block transition-metal trimers, from scandium to zinc. A search of the potential surfaces yields the following electronic ground states and bond lengths: Sc3(2A1',2.83 A), Ti3(7E',2.32 A), V3(2E",2.06 A), Cr3(17E',2.92 A), Mn3(16A2',2.73 A), Fe3(11E",2.24 A), Co3(6E",2.18 A), Ni3(3A2",2.23 A), Cu3(2E',2.37 A), and Zn3(1A1',2.93 A). Vibrational frequencies, several low-lying electronic states, and trends in bond lengths and atomization energies are discussed. The predicted dissociation energies DeltaE(M3-->M2+M) are 49.4 kcal mol(-1)(Sc3), 64.3 kcal mol(-1)(Ti3), 60.7 kcal mol(-1)(V3), 11.5 kcal mol(-1)(Cr3), 32.4 kcal mol(-1)(Mn3), 61.5 kcal mol(-1)(Fe3), 78.0 kcal mol(-1)(Co3), 86.1 kcal mol(-1)(Ni3), 26.8 kcal mol(-1)(Cu3), and 4.5 kcal mol(-1)(Zn3).

Journal Article↗
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↗
PubMed2005

The ground and two lowest-lying singlet excited electronic states of copper hydroxide (CuOH).

Various ab initio methods, including self-consistent field (SCF), configuration interaction, coupled cluster (CC), and complete-active-space SCF (CASSCF), have been employed to study the electronic structure of copper hydroxide (CuOH). Geometries, total energies, dipole moments, harmonic vibrational frequencies, and zero-point vibrational energies are reported for the linear 1Sigma+ and 1Pi stationary points, and for the bent ground-state X 1A', and excited-states 2 1A' and 1 1A". Six different basis sets have been used in the study, Wachters/DZP being the smallest and QZVPP being the largest. The ground- and excited-state bending modes present imaginary frequencies for the linear stationary points, indicating that bent structures are more favorable. The effects of relativity for CuOH are important and have been considered using the Douglas-Kroll approach with cc-pVTZ/cc-pVTZ_DK and cc-pVQZ/cc-pVQZ_DK basis sets. The bent ground and two lowest-lying singlet excited states of the CuOH molecule are indeed energetically more stable than the corresponding linear structures. The optimized geometrical parameters for the X 1A' and 1 1A" states agree fairly well with available experimental values. However, the 2 1A' structure and rotational constants are in poor agreement with experiment, and we suggest that the latter are in error. The predicted adiabatic excitation energies are also inconsistent with the experimental values of 45.5 kcal mol(-1) for the 2 1A' state and 52.6 kcal mol(-1) for the 1 1A" state. The theoretical CC and CASSCF methods show lower adiabatic excitation energies for the 1 1A" state (53.1 kcal mol(-1)) than those for the corresponding 2 1A' state (57.6 kcal mol(-1)), suggesting that the 1 1A" state might be the first singlet excited state while the 2 1A' state might be the second singlet excited state.

Journal Article↗
PubMed2005

The extremely flat torsional potential energy surface of oxalyl chloride.

The conformational behavior of oxalyl chloride has been investigated using ab initio Hartree-Fock (HF) and second-order Moller-Plesset (MP2) perturbation theories, and the coupled-cluster singles and doubles method appended with a perturbative inclusion of connected triple excitations [CCSD(T)]. Correlation consistent polarized valence quadruple-zeta (cc-pVQZ) and quintuple-zeta (cc-pV5Z) basis sets were used in this research. At the cc-pVQZ and cc-pV5Z HF levels, there is no stationary point corresponding to a stable gauche conformer. On the other hand, at the cc-pVQZ and cc-pV5Z MP2 levels and with the cc-pVQZ CCSD(T) method, the gauche conformer of oxalyl chloride was found at O[Double Bond]C-C[Double Bond]O dihedral angles of 81.9 degrees , 79.4 degrees , and 83.4 degrees , respectively. At the cc-pV5Z MP2 level, the energy barrier from trans to gauche was predicted to be 0.74 kcal mol(-1) and that from gauche to trans to be 0.09 kcal mol(-1). Thus, the potential-energy surface along the O[Double Bond]C-C[Double Bond]O torsional mode is exceedingly flat. The existence of the gauche conformation is mainly due to the minimization of steric repulsion.

Journal Article↗
PubMed2005

Application of equation-of-motion coupled-cluster methods to low-lying singlet and triplet electronic states of HBO and BOH.

The equilibrium structures and physical properties of the X (1)sigma(+) linear electronic states, linear excited singlet and triplet electronic states of hydroboron monoxide (HBO) (A (1)sigma(-), B (1)delta, a (3)sigma(+), and b (3)delta) and boron hydroxide (BOH) (A (1)sigma(+), B (1)Pi, and b (3)Pi), and their bent counterparts (HBO a (3)A('), b (3)A("), A (1)A("), B (1)A(') and BOH X (1)A('), b (3)A('), c (3)A("), A (1)A('), B (1)A('), C (1)A(")) are investigated using excited electronic state ab initio equation-of-motion coupled-cluster (EOM-CC) methods. A new implementation of open-shell EOM-CC including iterative partial triple excitations (EOM-CC3) was tested. Coupled-cluster wave functions with single and double excitations (CCSD), single, double, and iterative partial triple excitations (CC3), and single, double, and full triple excitations (CCSDT) are employed with the correlation-consistent quadruple and quintuple zeta basis sets. The linear HBO X (1)sigma(+) state is predicted to lie 48.3 kcal mol(-1) (2.09 eV) lower in energy than the BOH X (1)sigma(+) linear stationary point at the CCSDT level of theory. The CCSDT BOH barrier to linearity is predicted to lie 3.7 kcal mol(-1) (0.16 eV). With a harmonic zero-point vibrational energy correction, the HBO X (1)sigma(+)-BOH X (1)A(') energy difference is 45.2 kcal mol(-1) (1.96 eV). The lowest triplet excited electronic state of HBO, a (3)A('), has a predicted excitation energy (T(e)) of 115 kcal mol(-1) (4.97 eV) from the HBO ground state minimum, while the lowest-bound BOH excited electronic state, b (3)A('), has a T(e) of 70.2 kcal mol(-1) (3.04 eV) with respect to BOH X (1)A('). The T(e) values predicted for the lowest singlet excited states are A (1)A(")<--X (1)sigma(+)=139 kcal mol(-1) (6.01 eV) for HBO and A (1)A(')<--X (1)A(')=102 kcal mol(-1) (4.42 eV) for BOH. Also for BOH, the triplet vertical transition energies are b (3)A(')<--X (1)A(')=71.4 kcal mol(-1) (3.10 eV) and c (3)A(")<--X (1)A(')=87.2 kcal mol(-1) (3.78 eV).

Journal Article↗
PubMed2005

Ionization potentials of small lithium clusters (Lin) and hydrogenated lithium clusters (LinH).

We present accurate ionization potentials (IPs) for small lithium clusters and hydrogenated lithium clusters (n=1-4), computed using coupled-cluster singles and doubles theory augmented with a perturbative correction for connected triple excitations [CCSD(T)] with the correlation-consistent weighted core-valence quadruple-zeta basis set (cc-pwCVQZ). In some cases the full CCSDT method has been used. Comparison of computed binding energies with experiment for the pure cationic lithium clusters reveals excellent agreement, demonstrating that previous discrepancies between computed and experimentally derived atomization energies for the corresponding neutral clusters are due to the use of an inaccurate experimental IP for Li(4). The experimental IP for Li(4) falls 0.43 eV below our theoretical adiabatic value of 4.74 eV, which should be a lower bound to the measured IP. Our recommended zero-point corrected adiabatic IPs for Li, Li(2), Li(3), Li(4), LiH, Li(2)H, Li(3)H, and Li(4)H are 5.39, 5.14, 4.11, 4.74, 7.69, 3.98, 4.69, and 4.05 eV, respectively. Zero-point vibrationally corrected CCSD(T) atomization energies per atom for Li(2) (+), Li(3) (+), Li(4) (+), LiH(+), Li(2)H(+), Li(3)H(+), and Li(4)H(+) are 0.64, 0.96, 0.90, 0.056, 1.62, 1.40, and 1.40 eV, respectively.

Journal Article↗
PubMed2005

Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn- (n=1-8).

Developments in the preparation of new materials for microelectronics are focusing new attention on molecular systems incorporating several arsenic atoms. A systematic investigation of the As2Fn/As2Fn- systems was carried out using Density Functional Theory methods and a DZP++ quality basis set. Global and low-lying local geometric minima and relative energies are discussed and compared. The three types of neutral-anion separations reported in this work are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Harmonic vibrational frequencies pertaining to the global minimum for each compound are reported. From the first four studied species (As2Fn, n=1-4), all neutral molecules and their anions are shown to be stable with respect to As-As bond breaking. The neutral As2F molecule and its anion are predicted to have Cs symmetry. We find the trans F-As-As-F isomer of C2h symmetry and a pyramidalized vinylidene-like As-As-F2- isomer of Cs symmetry to be the global minima for the As2F2 and As2F2- species, respectively. The lowest lying minima of As2F3 and As2F3- are vinyl radical-like structures F-As-As-F2 of Cs symmetry. The neutral As2F4 global minimum is a trans-bent (like Si2H4) F2-As-As-F2 isomer of C2 symmetry, while its anion is predicted to have an unusual fluorine-bridged (C(1)) structure. The global minima of the neutral As2Fn species, n=5-8, are weakly bound complexes, held together by dipole-dipole interactions. All such structures have the AsFm-AsFn form, where (m,n) is (2,3) for As2F5, (3,3) for As2F6, (4,3) for As2F7), and (5,3) for As2F8. For As2F8 the beautiful pentavalent F4As-AsF4 structure (analogous to the stable AsF5 molecule) lies about 30 kcal/mol above the AsF3 . . . AsF5 complex. The stability of AsF(5) depends crucially on the strong As-F bonds, and replacing one of these with an As-As bond (in F4As-AsF4) has a very negative impact on the molecule's stability. The anions As2Fn-, n=5-8, are shown to be stable with respect to the As-As bond breaking, and we predict that all of them have fluorine-bridged or fluorine-linked structures. The zero-point vibrational energy corrected adiabatic electron affinities are predicted to be 2.28 eV (As2F), 1.95 eV (As2F2), 2.39 eV (As2F3), 1.71 eV (As2F4), 2.72 eV (As2F5), 1.79 eV (As2F6), 5.26 eV (As2F7), and 3.40 eV (As2F8) from the BHLYP method. Vertical detachment energies are rather large, especially for species with fluorine-bridged global minima, having values up to 6.45 eV (As2F7, BHLYP).

Journal Article↗
PubMed2005

Downfield proton chemical shifts are not reliable aromaticity indicators.

[structure: see text] The downfield chemical shifts of arene hydrogens (delta (1)H) are due only in part to the pi ring current contribution [sigma(//)(pi)]; local framework effects are equally important. Neither proton chemical shifts nor even sigma(||)(pi) tensor elements, per se, are reliable aromaticity indicators. Unsaturated polycyclic hydrocarbons with nonaromatic quinoid structures have delta (1)H and sigma(//)(pi) values in the "aromatic range". Conversely, numerous aromatic protons, including those in five-membered ring heterocycles, resonate in the "nonaromatic range".

Journal Article↗
PubMed2005

(G-H)*-C and G-(C-H)* radicals derived from the guanine.cytosine base pair cause DNA subunit lesions.

The radicals generated by the homolytic cleavage of an X-H bond from the guanine.cytosine (G.C) base pair were studied by using carefully calibrated theoretical methods. The gradient-corrected density functional B3LYP was applied in conjunction with double-zeta plus polarization and diffuse function basis sets. Optimized geometries, energies, and vibrational frequencies were obtained for all of the radicals considered. Structural perturbations along with energy relaxation due to radical formation were investigated. Dissociation energies of the G.C base pair and all of the radicals are predicted and compared with the dissociation energy of neutral G.C. The three lowest-energy base pair radicals all involve removal of an H atom from one of the N atoms in G.C. The lowest-energy base pair radical has the hydrogen atom removed from the guanine nitrogen atom used for the sugar phosphate linkage in DNA. This (G-H)(*)-C radical has a dissociation energy (to G-H(*) + C) of 30 kcal/mol, which may be compared with 27 kcal/mol for G.C. All of the radicals that are possible outcomes of direct ionizing radiation or oxidizing species were investigated for the presence of local minima with significant structural changes. Major structural deformations cause strain in the interstrand hydrogen bonding in the DNA double helix. Severe geometry changes were observed when the hydrogen was abstracted from interstrand hydrogen bonding sites, along with sizeable energy changes, indicating the potentially serious consequences to the G.C base pair.

Base Pairing↗
PubMed2005

The highly anharmonic BH5 potential energy surface characterized in the ab initio limit.

The strong sensitivity to level of theory of the salient features of the ground state potential energy surface of BH(5) has been overcome by rigorously converged ab initio computations employing correlation-consistent basis sets cc-p(C)VXZ (X=2-6), explicitly correlated R12 corrections, and coupled-cluster theory complete through quadruple excitations (CCSDTQ). Extrapolations via our focal point method yield a C(s)-symmetry global minimum of BH(3)-H(2) type featuring interfragment B-H distances of (1.401, 1.414) A, an H(2) bond length elongated to 0.803 A, and a BH(3)+H(2) dissociation energy D(e)(D(0))=6.6 (1.2) kcal mol(-1). The classical barriers for H(2) internal rotation and hydrogen scrambling are 0.07 and 5.81 kcal mol(-1), respectively, above the BH(5) minimum. Our thermochemical computations yield Delta(f)H(0) ( degrees )[BH(5)(g)]=-111.3+/-0.2 kcal mol(-1)+Delta(f)H(0) ( degrees )[B(g)], which is limited in accuracy only by persistent uncertainties in the enthalpy of formation of gaseous boron. As a first step in investigating the extremely anharmonic 12-dimensional vibrational dynamics of BH(5), a complete quartic force field has been computed at the all-electron cc-pCVQZ CCSD(T) level of theory. Previous matrix isolation infrared assignments of the nu(2) and nu(9) stretching modes of BH(5) compare favorably with our computed vibrational fundamentals, but the experimental assignment of the nu(6) bending mode of the BH(3) moiety is not supported by computed isotopic shifts.

Journal Article↗
PubMed2005

The singlet electronic ground state isomers of dialuminum monoxide: AlOAl, AlAlO, and the transition state connecting them.

The singlet electronic ground state isomers, X (1)Sigma(g) (+) (AlOAl D(infinityh)) and X (1)Sigma(+) (AlAlO C(infinitynu)), of dialuminum monoxide have been systematically investigated using ab initio electronic structure theory. The equilibrium structures and physical properties for the two molecules have been predicted employing self-consistent field (SCF) configuration interaction with single and double excitations (CISD), multireference CISD (MRCISD), coupled cluster with single and double excitations (CCSD), CCSD with perturbative triples [CCSD(T)], CCSD with iterative partial triple excitations (CCSDT-3 and CC3), and full triples (CCSDT) coupled cluster methods. Four correlation consistent polarized valence (cc-pVXZ) type basis sets were used. The AlAlO system is rather challenging theoretically. The two isomers are confirmed to have linear structures at all levels of theory. The symmetric isomer AlOAl is predicted to lie 81.9 kcal mol(-1) below the asymmetric isomer AlAlO at the cc-pV(Q+d)Z CCSD(T) level of theory. The predicted harmonic vibrational frequencies for the X (1)Sigma(g) (+) AlOAl molecule, omega(1)=517 cm(-1), omega(2)=95 cm(-1), and omega(3)=1014 cm(-1), are in good agreement with experimental values. The harmonic vibrational frequencies for the X (1)Sigma(+) AlAlO structure, omega(1)=1042 cm(-1), omega(2)=73 cm(-1), and omega(3)=253 cm(-1), presently have no experimental values with which to be compared. With the same methods the barrier heights for the isomerization AlOAl-->AlAlO and AlAlO-->AlOAl reactions were predicted to be 84.3 and 2.4 kcal mol(-1), respectively. The dissociation energies D(0) for AlOAl (X (1)Sigma(g) (+)) and AlAlO (X (1)Sigma(+))-->AlO (X (2)Sigma(+))+Al ((2)P) were determined to be 130.8 and 48.9 kcal mol(-1), respectively. Thus, both symmetric AlOAl (X (1)Sigma(g) (+)) and asymmetric AlAlO (X (1)Sigma(+)) isomers are expected to be thermodynamically stable with respect to the dissociation into AlO (X (2)Sigma(+)) + Al ((2)P) and kinetically stable for the isomerization reaction (AlAlO-->AlOAl) at sufficiently low temperatures.

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

Violation of the isolated square rule for group 13-15 oligomers: theoretical prediction of a new class of inorganic polymers.

It is widely thought that the oligomer compounds [RMYR]n (M-group 13, Y-group 15 element) should obey the isolated square rule found for the boron-nitrogen cages. In contrast to these expectations, the needle-shaped oligomers, which violate this rule, are more stable compared to the cage (fullerene-like) oligomers for all MY pairs (M = B, Al, Ga, In; Y = N, P, As). The stability of the needle-shaped clusters improves with increasing oligomerization degree. Thus, the isolated square rule, which is analogous to the isolated pentagon rule widely applied for fullerenes, should not serve as the basis for searches for the most stable structures of the inorganic oligomers. Generation of the needle-shaped oligomers from the group 13 and 15 hydrides is thermodynamically favorable. A synthesis of novel inorganic polymers, formed by fusion of trimeric M3Y3 rings, is expected to be viable.

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

The ab initio limit quartic force field of BH3.

The complete quartic force field of BH(3) has been converged to the ab initio limit by extrapolation of core-valence correlation-consistent basis set series (cc-pCVXZ, X = T, Q, 5) of all-electron CCSD(T) (coupled-cluster singles and doubles with perturbative triples) energy points. Additional computations including full coupled-cluster treatments through quadruple excitations (CCSDTQ), scalar relativistic effects, and diagonal Born-Oppenheimer corrections (DBOC) were concurrently executed. Within second-order vibrational perturbation theory (VPT2) our quartic force field yields the fundamental frequencies nu(1) = 2502.3 cm(-1), nu(2) = 1147.2 cm(-1), nu(3) = 2602.1 cm(-1), and nu(4) = 1196.5 cm(-1), in excellent agreement with observed gas-phase fundamentals, displaying a mean absolute error of only 0.3 cm(-1). Our converged prediction for the equilibrium bond length of BH(3) is r(e) = 1.1867 A.

Journal Article↗
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↗