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21.
An essential element of implicit solvent models, such as the generalized Born method, is a knowledge of the volume associated with the individual atoms of the solute. Two approaches for determining atomic volumes for the generalized Born model are described; one is based on Voronoi polyhedra and the other, on minimizing the fluctuations in the overall volume of the solute. Volumes to be used with various parameter sets for protein and nucleic acids in the CHARMM force field are determined from a large set of known structures. The volumes resulting from the two different approaches are compared with respect to various parameters, including the size and solvent accessibility of the structures from which they are determined. The question of whether to include hydrogens in the atomic representation of the solute volume is examined. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1857-1879, 2001 相似文献
22.
23.
Richardson NA Wesolowski SS Schaefer HF 《Journal of the American Chemical Society》2002,124(34):10163-10170
The adiabatic electron affinity (AEA) for the Watson-Crick guanine-cytosine (GC) DNA base pair is predicted using a range of density functional methods with double- and triple-zeta plus polarization plus diffuse (DZP++ and TZ2P++) basis sets in an effort to bracket the true electron affinity. The methods used have been calibrated against a comprehensive tabulation of experimental electron affinities (Chem.Rev. 2002, 102, 231). Optimized structures for GC and the GC anion are compared to the neutral and anionic forms of the individual bases as well as Rich's 1976 X-ray structure for sodium guanylyl-3',5'-cytidine nonahydrate, GpC.9H(2)O. Structural distortions and natural population (NPA) charge distributions of the GC anion indicate that the unpaired electron is localized primarily on the cytosine moiety. Unlike treatments using second-order perturbation theory (MP2), density functional theory consistently predicts a substantial positive adiabatic electron affinity for the GC pair (e.g., TZ2P++/B3LYP: +0.48 eV). The stabilization of C(-) via three hydrogen bonds to guanine is sufficient to facilitate adiabatic binding of an electron to GC and is also consistent with the positive experimental electron affinities obtained by photoelectron spectroscopy of cytosine anions incrementally microsolvated with water molecules. The pairing (dissociation) energy for GC(-) (35.6 kcal/mol) is determined with inclusion of electron correlation and shows the anion to have greater thermodynamic stability; the pairing energy for neutral GC (TZ2P++/B3LYP 23.9 kcal/mol) compares favorably to previous MP2/6-31G (23.4 kcal/mol) results and a debated experiment (21.0 kcal/mol). 相似文献
24.
Gonzales JM Barden CJ Brown ST Schleyer Pv Schaefer HF Li QS 《Journal of the American Chemical Society》2003,125(4):1064-1071
The adiabatic electron affinities of cyclopentadiene and 10 associated benzannelated derivatives have been predicted with both density functional and Hartree-Fock theory. These systems can also be regarded as benzenoid polycyclic aromatic hydrocarbons (PAHs) augmented with five-membered rings. Like the PAHs, the electron affinities of the present systems generally increase with the number of rings. To unequivocally bind an electron, cyclopentadiene must have at least two conventionally fused benzene rings. 1H-Benz[f]indene, a naphthalene-annulated cyclopentadiene, is predicted to have a zero-point energy corrected adiabatic electron affinity of 0.13 eV. Since the experimental E(A) of naphthalene is negative (-0.19 eV), the five-membered ring appendage contributes to the stability of the naphthalene-derived 1H-benz[f]indene radical anion significantly. The key to binding the electron is a contiguous sequence of fused benzenes, since fluorene, the isomer of 1H-benz[f]indene, with separated six-membered rings, has an electron affinity of -0.07 eV. Each additional benzene ring in the sequence fused to cyclopentadiene increases the electron affinity by 0.15-0.65 eV: the most reliable predictions are cyclopentadiene (-0.63 eV), indene (-0.49 eV), fluorene (-0.07 eV), 1H-benz[f]indene (0.13 eV), 1,2-benzofluorene (0.25 eV), 2,3-benzofluorene (0.26 eV), 12H-dibenzo[b,h]fluorene (0.65 eV), 13H-indeno[1,2-b]anthracene (0.82 eV), and 1H-cyclopenta[b]naphthacene (1.10 eV). In contrast, if the six-membered ring-fusion is across the C(2)-C(3) cyclopentadiene single bond, only a single benzene is needed to bind an electron. The theoretical electron affinity of the resulting molecule, isoindene, is 0.49 eV, and this increases to 1.22 eV for 2H-benz[f]indene. The degree of aromaticity is responsible for this behavior. While the radical anions are stabilized by conjugation, which increases with the size of the system, the regular indenes, like PAHs in general, suffer from the loss of aromatic stabilization in forming their radical anions. While indene is 21 kcal mol(-1) more stable than isoindene, the corresponding radical anion isomers have almost the same energy. Nucleus-independent chemical shift calculations show that the highly aromatic molecules lose almost all aromaticity when an extra electron is present. The radical anions of cyclopentadiene and all of its annulated derivatives have remarkably low C-H bond dissociation energies (only 18-34 kcal mol(-1) for the mono-, bi-, and tricyclics considered). Hydrogen atom loss leads to the restoration of aromaticity in the highly stabilized cyclopentadienyl anion congeners. 相似文献
25.
K. -P. Arnold K. -P. Döring M. Gladisch N. Haas D. Herlach W. Jacobs M. Krauth S. Liebke H. Metz H. Orth H. -E. Schaefer A. Seeger 《Hyperfine Interactions》1984,17(1-4):219-224
We have measured the transverse spin relaxation of positive muons
+ in Al single crystals after irradiation at 150 K with 3 MeV electrons. The relaxation functions agree with those expected for diffusion-limited trapping of the
+ in monovacancies. Between 215 K and 60 K the
+ diffusivity is well described by the Flynn-Stoneham law (multi-phonon incoherent tunnelling between ground states) with an activation enthalpyH
a = (30±2) meV. At lower temperatures, few-phonon (in particular one-phonon) processes become important. The decrease of the vacancy concentration by a factor of 100 during annealing between 227 K and 267 K has been studied. 相似文献
26.
Joachim Schaefer William A. Lester Donald Kouri Charles A. Wells 《Chemical physics letters》1974,24(2):185-190
Integral cross sections for pure rotational and vibrational-rotational excitation of H2(X1Σ+g) by Li+(1S) impact are computed by close-coupling methods at 0.2, 0.6, and 1.2 eV in the c.m. system using vibrational functions that are numerical solutions of the one-dimensional radial Schrödinger equation for harmonic, Morse, and adiabatically corrected Kolos-Wolniewicz (KW) potential functions. Comparison of results employing KW and Morse functions shows excellent agreement for all transitions studied. Findings using harmonic oscillator functions, however, differ noticeably from KW and Morse values for vibrational (0 → 1) and very large rotational (Δj = 10) transitions, but are satisfactory for lower order (0 → 2, 4, 6, 8) rotational transitions. 相似文献
27.
Donald R. McLaughlin Charles F. Bender Henry F. Schaefer III 《Theoretical chemistry accounts》1972,25(4):352-359
Ab initio calculations including electron correlation are reported for the water and methylene molecules as a function of geometry. A large contracted gaussian basis set is used and the multiconfiguration wave functions, optimized by the iterative natural orbital procedure, include 277 and 617 configurations for H2O and CH2 respectively. The method of selecting configurations, yielding first-order wave functions, is discussed in some detail. For H2O, the SCF geometry is r=0,942 Å, =105,8°, the correlated result is r=0,968 Å, =103,2°, and the experimental r=0,957 Å, =104,5°. The water stretching force constants, in millidynes/Å, are 8,72 (SCF), 8,75 (CI), and 8,4 (experiment). Bending force constants are 0,88 (SCF), 0,83 (CI), and 0,76 (experiment). For methylene the SCF geometry is r=1,072 Å, =129,5°, while the result from first-order wave functions is r=1,088 Å, =134°. The predicted CH2 force constants are 6,16 (SCF) and 6,13 (CI) for stretching and 0,44 (SCF) and 0,33 (CI) for bending.
Work performed under the auspices of the U.S. Atomic Energy Commision.
Supported by the grants from the Research Corporation and the University of California Committee on Research. 相似文献
Zusammenfassung Es wird über ab intito-Rechnungen mit Berücksichtigung der Elektronenkorrelation berichtet, die an Wasser- und Methylenmolekülen als Funktion der Geometrie durchgeführt worden sind. Dazu benutzt man einen großen kontrahierten Gauß-Basissatz. Die Multikonfigurationswellenfunktionen, die unter Benutzung von natürlichen Orbitalen nach der iterativen Prozedur optimiert werden, enthalten für H2O 277 Konfigurationen und für CH2 617. Die Auswahlmethode, die zu Wellenfunktionen 1. Ordnung führt, wird diskutiert. Im Falle des Wassers erhält man die SCF-Geometrie zu r=0,942 Å, =105,8°, das korrelierte Resultat ist: r=0,968 Å, =103,2° und das experimentelle r=0,957 Å, =104,5°. Für Wasser ergeben sich die Valenzkraftkonstanten (in Millidyn Å–1) 8,72 (SCF), 8,75 (CI) und 8,4 (Experiment). Die Deformationskonstanten sind 0,88 (SCF), 0,83 (CI) und 0,76 (Experiment). Im Falle des Methylens ist die SCF-Geometrie r=1,072 Å, =129,5°, während man mit Wellenfunktionen 1. Ordnung r=1,088 Å und =134° erhält. Die CH2-Kraftkonstanten werden für die Valenzschwingung zu 6,16 (SCF) und 6,13 (CI) bzw. für die Deformationsschwingung zu 0,44 (SCF) und 0,33 (CI) vorausgesagt.
Work performed under the auspices of the U.S. Atomic Energy Commision.
Supported by the grants from the Research Corporation and the University of California Committee on Research. 相似文献
28.
Highly correlated coupled cluster methods with single and double excitations (CSSD) and CCSD with perturbative triple excitations were used to predict molecular structures and harmonic vibrational frequencies for the electronic ground state X 1Sigma+, and for the 3Delta, 3Sigma+, 3Phi, 1 3Pi, 2 3Pi, 1Sigma+, 1Delta, and 1Pi excited states of NiCO. The X 1Sigma+ ground state's geometry is for the first time compared with the recently determined experimental structure. The adiabatic excitation energies, vertical excitation energies, and dissociation energies of these excited states are predicted. The importance of pi and sigma bonding for the Ni-C bond is discussed based on the structures of excited states. 相似文献
29.
Neutral anion energy differences for a large class of alpha-substituted silyl radicals have been computed to determine the effect of alkyl, silyl, and halo substituents on their electron affinities. In particular, we report theoretical predictions of the adiabatic electron affinities (AEAs), vertical electron affinities (VEAs), and vertical detachment energies (VDEs) for a series of methyl-, silyl-, and halo-substituted silyl radical compounds. This work utilizes the carefully calibrated DZP++ basis set, in conjunction with the pure BLYP and OLYP functionals, as well as with the hybrid B3LYP, BHLYP, PBE1PBE, MPW1K, and O3LYP functionals. Bromine has the largest effect in stabilizing the anions, and the BLYP/DZP++ AEA for SiBr(3) is 3.29 eV. The other predicted electron affinities are for SiH(3) (1.37 eV), SiH(2)CH(3) (1.09 eV), SiH(2)F (1.54 eV), SiH(2)Cl (1.94 eV), SiH(2)Br (2.05 eV), SiH(2)(SiH(3)) (1.77 eV), SiH(CH(3))(2) (0.92 eV), SiHF(2) (1.86 eV), SiHCl(2) (2.53 eV), SiHBr(2) (2.67 eV), Si(CH(3))(3) (0.86 eV), SiF(3) (2.66 eV), SiCl(3) (3.21 eV), Si(SiH(3))(3) (2.25 eV), and SiFClBr (3.13 eV). For the five silyl radicals where experimental data are available, the BLYP functional gives the most accurate determination of AEAs; the average absolute error is 0.04(1) eV, whereas the corresponding errors for the O3LYP, MPW1K, PBE1PBE, B3LYP, OLYP, and BHLYP functionals are 0.05(8), 0.06(0), 0.06(3), 0.08(5), 0.11(5), and 0.15(3) eV, respectively. 相似文献
30.
A novel solid-phase synthesis of thalidomide and its metabolites and analogues is described. The synthetic strategy involves the coupling of hydroxymethyl polystyrene with phthalic anhydride to form the resin-linked acid. The acid is then reacted with primary amines followed by acid or base treatment to form thalidomide and its analogues with either open or closed phthalimide rings. Most of the analogues are synthesized with high yields (40.3-98.1% in three steps) and purities (92.3-98.9%). 相似文献