PubMed Health⌕ Search

Biomedical subjects

Henry F Schaefer

Publications and source records attributed to Henry F Schaefer.

At least 37 records · Page 2Linked to original sources
PubMed2006

Microsolvation effects on the electron capturing ability of thymine: thymine-water clusters.

The effects of solvation on the stability of thymine and its negative ion have been investigated by explicitly considering the structures of complexes of thymine with up to five water molecules and the respective anions at the B3LYP/DZP++ level of theory. The vertical detachment energy of thymine was predicted to increase gradually with the hydration number, consistent with experimental observations from a photodetachment-photoelectron spectroscopy study J. Schiedt et al., [Chem. Phys. 239, 511 (1998)]. The adiabatic electron affinity of thymine was also found to increase with the hydration number, which implies that while the conventional valence anion of thymine is only marginally bound in the gas phase, it may form a stable anion in aqueous solution.

Anions↗
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

The deprotonated guanine-cytosine base pair.

Awareness of the harmful effects of radiation has increased interest in finding the mechanisms of DNA damage. Radical and anion formation among the DNA base pairs are thought to be important steps in such damage [Collins, G. P. (2003) Sci. Am. 289 (3), 26-27]. Energetic properties and optimized geometries of 10 radicals and their respective anions derived through hydrogen abstraction from the Watson-Crick guanine-cytosine (G-C) base pair have been studied using reliable theoretical methods. The most favorable deprotonated structure (dissociation energy 42 kcal x mol(-1), vertical detachment energy 3.79 eV) ejects the proton analogous to the cytosine glycosidic bond in DNA. This structure is a surprisingly large 12 kcal x mol(-1) lower in energy than any of the other nine deprotonated G-C structures. This system retains the qualitative G-C structure but with the H...O2 distance dramatically reduced from 1.88 to 1.58 A, an extremely short hydrogen bond. The most interesting deprotonated G-C structure is a "reverse wobble" incorporating two N-H...N hydrogen bonds. Three different types of relaxation energies (4.3-54 kcal x mol(-1)) are defined and reported to evaluate the energy released via different mechanisms for the preparation of the deprotonated species. Relative energies, adiabatic electron affinities (ranging from 1.93 to 3.65 eV), and pairing energies are determined to discern which radical will most alter the G-C properties. The most stable deprotonated base pair corresponds to the radical with the largest adiabatic electron affinity, 3.65 eV. This value is an enormous increase over the electron affinity (0.60 eV) of the closed-shell G-C base pair.

Base Pairing↗
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

Mindless chemistry.

Applications of an automated stochastic search procedure for locating all possible minima with a given composition are illustrated by the pentatomic molecules BCNOS, CAlSiPS, C(4)B(-), C(4)Al(-), and CBe(4)(2-), as well as by C(6)Be, the C(6)Be(2-) dianion, and C(6)H(2). All previously identified minima were reproduced, and many new structures, often with nonintuitive geometries, were found.

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

Protonated carbonyl sulfide: prospects for the spectroscopic observation of the elusive HSCO+ isomer.

Spurred by the apparent conflict between ab initio predictions and infrared spectroscopic evidence regarding the relative stability of isomers of protonated carbonyl sulfide, key stationary points on the isomerization surface of HOCS(+) have been examined via systematic extrapolations of ab initio energies. Electron correlation has been accounted for using second-order Møller-Plesset perturbation theory and coupled cluster theory through triple excitations [CCSD, CCSD(T), and CCSDT] in conjunction with the correlation consistent hierarchy of basis sets, cc-pVXZ (X=D,T,Q,5,6). HSCO(+) is predicted to lie lower in energy than HOCS(+) by 4.86 kcal mol(-1), computed using the focal point extrapolation scheme of Allen and co-workers [J. Chem. Phys. 99, 4638 (1993)] with corrections for anharmonic zero-point vibrational energy, core correlation, non-Born-Oppenheimer, and scalar relativistic effects. A transition state has been located, constituting the barrier to isomerization of HSCO(+) to HOCS(+), lying 68.9 kcal mol(-1) higher in energy than HSCO(+). This is well above predicted exothermicity [DeltaH(r) (o)(0 K)=48.1 kcal mol(-1), cc-pVQZ CCSD(T)] for the reaction considered in the experiments (HSCO(+)+H(2)-->OCS+H(3) (+)). Though proton tunneling will lead to a lower effective barrier, this prediction is consistent with the lack of HSCO(+) in electrical discharges in H(2)OCS, since the relative populations of HOCS(+) and HSCO(+) will depend on the experimental details of the protonation route rather than the relative thermodynamic stability of the isomers. Anharmonic vibrational frequencies and vibrationally corrected rotational constants from cc-pVTZ CCSD(T) cubic and quartic force constants are provided, to aid in the spectroscopic observation of the energetically favorable but apparently elusive HSCO(+) isomer.

Journal Article↗
PubMed2006

The small planarization barriers for the amino group in the nucleic acid bases.

The amino group in the nucleic acid bases frequently interacts with other bases or with other molecular systems. Thus any nonplanarity of the amino group may affect the molecular recognition of nucleic acids. Ab initio Hartree-Fock (HF) and second-order Moller-Plesset perturbation (MP2) levels of theory have been used to obtain the equilibrium geometries of the C(l) and C(s) structures for five common nucleic acid bases. The energy barriers between the C(l) and C(s) structures have also been predicted. A series of correlation consistent basis sets up to cc-pCVQZ and aug-cc-pVQZ has been used to systematically study the dependence of the amino group nonplanarity. The equilibrium geometries of the nucleic acid bases with an amino group, including adenine, guanine, and cytosine, are examined carefully. At the MP2 level of theory, larger basis sets decrease the extent of nonplanarity of the amino group, but the decrease slows down when the QZ basis sets are used, demonstrating the intrinsic property of nonplanarity for guanine. For adenine and cytosine the situation is less clear; as the HF limit is approached, these two structures become planar. Addition of core correlation effects or diffuse functions further decreases the degree of nucleic acid base nonplanarity, in comparison to the original cc-pVXZ (X=D, T, and Q) basis sets. The aug-cc-pVXZ basis shows smaller degrees of nonplanarity than the cc-pCVXZ sets. The aug-cc-pVXZ basis is less size dependent than the cc-pVXZ and cc-pCVXZ sets in the prediction of the amino-group-related bond angles and dihedral angles and energy barriers for adenine, guanine, and cytosine. The cc-pCVQZ and aug-cc-pVQZ MP2 results may be regarded as benchmark predictions for the five common bases. The predicted classical barriers to planarization are 0.02 (adenine), 0.74 (guanine), and 0.03(cytosine) kcal mol(-1).

Adenine↗
PubMed2006

Characterization of the X2A1, A2B1, and X2Pi electronic states of the Ga2H molecule and the X2A' and A 2A" isomerization transition states connecting the three minima.

A wide range of highly correlated ab initio methods has been used to predict the geometrical parameters of the linear (X (2)Pi) and H-bridged (X (2)A(1) and A (2)B(1)) Ga(2)H isomers and two isomerization transition states (X (2)A(') and A (2)A(")) connecting the three minima. Dipole moments and vibrational frequencies are also obtained. The global minimum X (2)A(1) ground state of the H-bridged GaHGa isomer is predicted to lie only 1.6 [1.9 with the zero-point vibrational energy (ZPVE) corrections] kcal mol(-1) below the A (2)B(1) state. The X (2)A(1) state lies 5.4 kcal mol(-1) below the X (2)Pi ground state of the linear GaGaH isomer at the coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)] level of theory with the augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set. The full triples coupled-cluster method is found to alter these CCSD(T) predictions by as much as 0.3 kcal mol(-1). The forward isomerization barriers from the linear ground state to the X (2)A(') and A (2)A(") transition states are determined to be 3.3 and 5.3 kcal mol(-1), respectively. The reverse isomerization barrier between the X (2)A(1) GaHGa structure and the X (2)Pi GaGaH structure is predicted to be 8.6 (8.2 with the ZPVE corrections) kcal mol(-1) at the aug-cc-pVQZ CCSD(T) level of theory.

Journal Article↗
PubMed2006

The low-lying electronic states of nickel cyanide and isocyanide: A theoretical investigation.

At different levels of coupled cluster theory optimum structures, energetics, and harmonic vibrational frequencies for several low-lying doublet and quartet electronic states of linear NiCN and NiNC were studied using four contracted Gaussian basis sets, ranging from Ni[6s5p4d2f], CN[4s3p2d] to Ni[8s7p5d3f2g1h], CN[5s4p3d2f1g]. The most reliable predictions were obtained with a relativistic Douglas-Kroll restricted open-shell-based coupled cluster method including singles, doubles, and perturbative triple excitations [DK-R/UCCSD(T)]. This level of theory was used in conjunction with correlation-consistent polarized valence Douglas-Kroll recontracted quadruple-zeta basis sets (cc-pVQZDK). The energetic ordering of the electronic states of NiCN is predicted to be 2delta < 2sigma+ < 2pi < 4delta < 4pi and that of NiNC is 2delta approximately 2sigma+ < 2pi < 4delta < 4pi < 4sigma-. Our theoretical investigation supports the assignment of the ground-state term symbol, the Ni-C stretching frequency, and the bending frequency for the ground electronic state of NiCN by Kingston et al. [J. Mol. Spectrosc. 215, 106 (2002)] and by Sheridan and Ziurys [J. Chem. Phys. 118, 6370 (2003)]. The predicted structure of the 2delta ground state of NiCN, r(e)(Ni-C) = 1.822 angstroms and r(e)(C-N) = 1.167 angstroms, at DK-R/UCCSD(T)/cc-pVQZDK shows excellent agreement with the experimentally determined Ni-C bond length of 1.826 A and less satisfactory agreement for the C-N bond length of 1.153 angstroms [J. Chem. Phys. 118, 6370 (2003)]. It is also concluded that the metal-to-ligand pi back donation is weak or negligible. Additionally, we found that on the 2delta surface the linear cyanide isomer lies lower in energy than the linear isocyanide isomer by 12.2 kcal mol(-1).

Journal Article↗
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

Mechanism of the aminolysis of methyl benzoate: a computational study.

Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.

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

Model identity SN2 reactions CH3X + X- (X = F, Cl, CN, OH, SH, NH2, PH2): Marcus theory analyzed.

The structures of seven gas phase identity S(N)2 reactions of the form CH(3)X + X(-) have been characterized with seven distinct theoretical methods: RHF, B3LYP, BLYP, BP86, MP2, CCSD, and CCSD(T), in conjunction with basis sets of double and triple zeta quality. Additionally, the energetics of said reactions have been definitively computed using focal point analyses utilizing extrapolation to the one-particle limit for the Hartree-Fock and MP2 energies using basis sets of up to aug-cc-pV5Z quality, inclusion of higher order correlation effects [CCSD and CCSD(T)] with basis sets of aug-cc-pVTZ quality, and additional auxiliary terms for core correlation and scalar relativistic effects. Final net activation barriers for the reactions are E(b)(F,F)= -0.8, E(b)(Cl,Cl)= 1.6, E(b)(CN,CN)= 28.7, E(b)(OH,OH)= 14.3, E(b)(SH,SH)= 13.8, E(b)(NH2,NH2)= 28.6, and E(b)(PH2,PH2)= 25.7 kcal mol(-1). General trends in the energetics, specifically the performance of the density functionals, and the component energies of the focal point analyses are discussed. The utility of classic Marcus theory as a technique for barrier predictions has been carefully analyzed. The standard Marcus theory results show disparities of up to 9 kcal mol(-1) with respect to explicitly computed results. However, when alternative approaches to Marcus theory, independent of the well-depths, are considered, excellent performance is achieved, with the largest deviations being under 3 kcal mol(-1).

Journal Article↗
PubMed2005

Does GaH5 exist?

The existence or nonexistence of GaH(5) has been widely discussed [N. M. Mitzel, Angew. Chem. Int. Ed. 42, 3856 (2003)]. Seven possible structures for gallium pentahydride have been systematically investigated using ab initio electronic structure theory. Structures and vibrational frequencies have been determined employing self-consistent field, coupled cluster including all single and double excitations (CCSD), and CCSD with perturbative triples levels of theory, with at least three correlation-consistent polarized-valence-(cc-pVXZ and aug-cc-pVXZ) type basis sets. The X (1)A(') state for GaH(5) is predicted to be weakly bound complex 1 between gallane and molecular hydrogen, with C(s) symmetry. The dissociation energy corresponding to GaH(5)-->GaH(3)+H(2) is predicted to be D(e)=2.05 kcal mol(-1). The H-H stretching fundamental is predicted to be v=4060 cm(-1), compared to the tentatively assigned experimental feature of Wang and Andrews [J. Phys. Chem. A 107, 11371 (2003)] at 4087 cm(-1). A second C(s) structure 2 with nearly equal energy is predicted to be a transition state, corresponding to a 90 degrees rotation of the H(2) bond. Thus the rotation of the hydrogen molecule is essentially free. However, hydrogen scrambling through the C(2v) structure 3 seems unlikely, as the activation barrier for scrambling is at least 30 kcal mol(-1) higher in energy than that for the dissociation of GaH(5) to GaH(3) and H(2). Two additional structures consisting of GaH(3) with a dihydrogen bond perpendicular to gallane (C(3v) structure 4) and an in-plane dihydrogen bond [C(s)(III) structure 5] were also examined. A C(3v) symmetry second-order saddle point has nearly the same energy as the GaH(3)+H(2) dissociation limit, while the C(s)(III) structure 5 is a transition structure to the C(3v) structure. The C(4v) structure 6 and the D(3h) structure 7 are much higher in energy than GaH(3)+H(2) by 88 and 103 kcal mol(-1), respectively.

Journal Article↗
PubMed2005

The pentacyanocyclopentadienyl system: structures and energetics.

In light of the recent silylation route to protonated pentacyanocyclopentadienyl (PCCp) anion reported by Richardson and Reed, PCCp anion, neutral radical, and protonated species have been investigated theoretically. The predicted adiabatic electron affinity for PCCp (ZPVE-corrected value in parentheses) is enormous, 5.56 (5.47) eV. As with the unsubstituted cyclopentadienyl radical, the PCCp radical exhibits a Jahn-Teller distortion from the D(5)(h) symmetry of the aromatic anion, yielding five equivalent (2)B(2) minima that should show uninhibited pseudorotation about a D(5)(h) conical intersection. Formation of the conjugate acid occurs via protonation of the anion at a nitrile nitrogen, which is favored over protonation at a ring carbon by 6.5 kcal/mol, with the preference explained by retention of aromaticity upon protonation at the nitrogen. Possible acid dimer structures have been investigated to evaluate the proposed polymeric acid structure of Richardson and Reed. Our predictions confirm their suggested polymeric structure, but we also present an alternative, self-contained dimer that should be competitive kinetically and thermodynamically. Vibrational frequencies and infrared intensities are predicted, to aid in the experimental identification of several of these species.

Anions↗