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1.
Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.  相似文献   

2.
To avoid the solution of numerous Kohn–Sham one-body potential equations for wave functions in density functional theory, various groups independently proposed the use of Pauli potential to bosonise the customary one-body potential theory. Here, we utilise our recent quantum Monte Carlo calculations of the ground-state electron density of the Be atom to estimate the bosonised one-body potential VB(r) and hence extract the Pauli potential for this atom.  相似文献   

3.
Calculations are carried out using first-principles self-consistent local-density and nonlocal density theory of the electronic structure, the total energy, and the charge density of a variety of semiconducting and insulating compounds under hydrostatic and uniaxial pressure. For several cases, the transition pressure from one structure to another is determined as well as the pressure coefficients of the main band gaps. It is shown that several properties are calculated with adequate accuracy to be compared with experiment, so that values which have not yet been measured are trustworthy predictions. © 1995 John Wiley & Sons, Inc.  相似文献   

4.
Photochemical profiles of omega-cleavage of carbon-X (X = Br and Cl) bonds in m-bromo- and m-chloromethylbenzophenones (m-BMBP and m-CMBP) were investigated by laser photolysis techniques and DFT calculations. m-BMBP and m-CMBP were found to undergo omega-bond cleavage to yield the m-benzoylbenzyl radical (m-BBR) at 295 K, and the quantum yields were determined. No CIDEP signal was detected upon 308 nm laser photolysis of both the compounds. From these observations, it was inferred that the omega-bond of these m-halomethylbenzophenones (m-HMBP) cleaves in the lowest excited singlet state (S(1)(n,pi(*))) upon direct excitation. Upon triplet sensitization of acetone (Ac), the m-BBR formation was observed in transient absorption for an Ac-m-BMBP system, and an efficiency of the C-Br bond cleavage in the lowest triplet state (T(1)(n,pi(*))) of m-BMBP was determined. In contrast, formation of triplet m-CMBP was seen for an Ac-m-CMBP system. Absence of C-Cl bond cleavage in the triplet state of m-CMBP indicated the reactive state of m-CMBP for omega-cleavage is only the S(1)(n,pi(*)) state. Based on the efficiencies and DFT calculations for excited state energies, photoinduced omega-bond dissociation of m- and p-HMBPs was characterized.  相似文献   

5.
The FSGO quantum mechanical model is used to makeab initio calculations of the geometrical structures and energies of the ground state configurations of the octahydrotriborate anion, B3H 8 , and tetraborane, B4H10. Both molecules are assumed to belong to theC 2v symmetry point group during these computations. Comparisons with available experimental data show good agreement. B4H10 calculations are also compared with results of SCF calculations.  相似文献   

6.
The solvation structure of the lithium ion in room-temperature ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl) imide (EMI(+)TFSI(-)) and N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (BMP(+0TFSI(-)) has been studied by Raman spectroscopy and DFT calculations. Raman spectra of EMI(+)TFSI(-) and BMP(+)TFSI(-) containing Li(+)TFSI(-) over the range 0.144-0.589 and 0.076-0.633 mol dm(-3), respectively, were measured at 298 K. A strong 744 cm-1 band of the free TFSI(-) ion in the bulk weakens with increasing concentration of the lithium ion, and it revealed by analyzing the intensity decrease that the two TFSI(-) ions bind to the metal ion. The lithium ion may be four-coordinated through the O atoms of two bidentate TFSI(-) ions. It has been established in our previous work that the TFSI(-) ion involves two conformers of C(1) (cis) and C(2) (trans) symmetries in equilibrium, and the dipole moment of the C(1) conformer is significantly larger than that of the C(2) conformer. On the basis of these facts, the geometries and SCF energies of possible solvate ion clusters [Li(C(1)-TFSI(-))(2)](-), [Li(C(1)-TFSI(-))(C(2)-TFSI(-))](-), and [Li(C(2)-TFSI(-))(2)](-) were examined using the theoretical DFT calculations. It is concluded that the C(1) conformer is more preferred to the C(2) conformer in the vicinity of the lithium ion.  相似文献   

7.
The structure of bis(trifluoromethanesulfonyl) imide (TFSI-) in the liquid state has been studied by means of Raman spectroscopy and DFT calculations. Raman spectra of 1-ethyl-3-methylimidazolium (EMI+) TFSI- show relatively strong bands arising from TFSI- at about 398 and 407 cm(-1). Interestingly, the 407 cm(-1) band, relative to the 398 cm(-1) one, is appreciably intensified with raising temperature, suggesting that an equilibrium is established between TFSI- conformers in the liquid state. According to DFT calculations followed by normal frequency analyses, two conformers of C2 and C1 symmetry, respectively, constitute global and local minima, with an energy difference 2.2-3.3 kJ mol(-1). The wagging omega-SO2 vibration appears at 396 and 430 cm(-1) for the C1 conformer and at 387 and 402 cm(-1) for the C2 one. Observed Raman spectra over the range 380-440 cm(-1) were deconvoluted to extract intrinsic bands of TFSI- conformers, and the enthalpy of conformational change from C2 to C1 was evaluated. The enthalpy value is in good agreement with that obtained by theoretical calculations. We thus conclude that a conformational equilibrium is established between the C1 and C2 conformers of TFSI- in the liquid EMI+TFSI-, and the C2 conformer is more favorable than the C1 one.  相似文献   

8.
Calculations at the SCF level and with inclusion of correlation were carried out on a portion of the potential 1A′ state of the cyclopropenyl anion which was found to be nonplanar in its most stable geometry.  相似文献   

9.
On the basis of a thorough Cambridge Structural Database survey, we present a statistical analysis of the packing of TCNQ anion pi-radicals in TCNQ charge transfer salts, which reveals three packing motifs between neighboring TCNQs: one with a zero longitudinal offset and an approximate 1 A transversal offset, another with an approximate 2 A longitudinal offset and zero transversal offset, and the third with a relatively long sigma-bond in the length of r = 1.6-1.7 A connecting two TCNQ fragments. Along with the statistical analysis of the crystal structures, we also present density functional theory calculations of the total energy, covalent pi-pi bonding interaction energy, and Coulombic repulsion energy for the [TCNQ](2)(2-)pi-dimers with various packing geometries. We find that the interactions between TCNQ anion pi-radicals include contributions from intermolecular covalent pi-pi bonding interaction and local dipole repulsions, in addition to Coulombic repulsion, van der Waals and the attractive electrostatic forces between counter-cations and TCNQ anions pointed out recently by other groups for TCNE anion radicals. We describe an approximate formula for intermolecular interaction energy, E(int) = E(coul) + E(bond) + E(vdW), for systems in vacuum, while in the solid state E(coul) is compensated by the attractive electrostatic forces between counter-cations and TCNQ anions. We conclude that the crystal packing of TCNQ molecules in their charge transfer salts is predominantly determined by the intermolecular covalent pi-pi bonding term, E(bond).  相似文献   

10.
11.

Abstract  

We performed density functional theory calculations for nitrogen-doped models of the representative structures of (6,0) zigzag and (4,4) armchair aluminum phosphide nanotubes (AlPNTs). Our results indicate that the optimized bond distances and tip diameters do not detect the effects of the N-doped regions; however, the effects are observed for the band gap energies and dipole moments. It is noted that substitution of the P atom by the N atom does not influence the value of band gap energy for this N-doped model. The results also indicate that the tendency of the Al atom for contribution to the Al–N bond is stronger than the tendency of the P atom for contribution to the N–P bond; therefore, the latter form of substitution makes the AlPNTs interesting as reactive materials towards other atoms or molecules, especially for the the zigzag AlPNT.  相似文献   

12.
13.
An approach is proposed to reduce the computational effort required for solving Kohn–Sham equation through rejecting some unoccupied orbitals with negligible influence on the total energy in the process of iteration. A formula has been derived to estimate the error of the total energy resulted from rejecting some unoccupied orbitals and it is used to set up the threshold for rejection of orbitals. The method has been tested with several representative molecules as samples and the obtained result is satisfactory.  相似文献   

14.
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16.
The B3LYP and B3PW91 density functionals were employed with a large [BS1 = 6-311+G(3df,2p)] and small [BS2 = 6-311G(d,p)] basis set to compute enthalpies of formation (at optimized MP2/6-31G(d) geometries and with scaled HF/6-31G(d) frequencies) in the following series of haloalkanes: (1) the 15 fluoro-, chloro-, and chlorofluoromethanes, (2) the 18 fluorinated and chlorinated ethanes. Similar to earlier higher level calculations on haloalkanes, the computed enthalpies exhibited very large, systematic deviations from experiment. It was found that these errors could be largely eliminated using a very simple Bond Additivity Correction (BAC) formula, Delta(f)H degrees (BAC) = Delta(f)H degrees (calc) - n(CX). Delta(CX) [X = F, Cl], in which the BAC parameters, Delta(CF) and Delta(CCl) were determined by fitting the equation to experimental data on the four fluoroethanes and chloroethanes, respectively. The resultant BAC corrected enthalpies of formation are in excellent agreement with experiment, with RMS deviations in the same range as quoted RMS errors in measured enthalpies. Therefore, this simple BAC procedure may be utilized to provide reliable semiquantitative estimates of enthalpies of formation in larger haloalkanes, for which higher level ab initio calculations are not feasible.  相似文献   

17.
Accurate ab initio Cl calculations of interaction energies for He-He are shown to continue to be invaluable for the interpretation and assessment of experimental data for this system in both the low-and high-energy, part of the repulsive wall.  相似文献   

18.
A valence-type anion of the canonical tautomer of uracil has been characterized using explicitly correlated second-order Moller-Plesset perturbation theory (RI-MP2-R12) in conjunction with conventional coupled-cluster theory with single, double, and perturbative triple excitations. At this level of electron-correlation treatment and after inclusion of a zero-point vibrational energy correction, determined in the harmonic approximation at the RI-MP2 level of theory, the valence anion is adiabatically stable with respect to the neutral molecule by 40 meV. The anion is characterized by a vertical detachment energy of 0.60 eV. To obtain accurate estimates of the vertical and adiabatic electron binding energies, a scheme was applied in which electronic energy contributions from various levels of theory were added, each of them extrapolated to the corresponding basis-set limit. The MP2 basis-set limits were also evaluated using an explicitly correlated approach, and the results of these calculations are in agreement with the extrapolated values. A remarkable feature of the valence anionic state is that the adiabatic electron binding energy is positive but smaller than the adiabatic electron binding energy of the dipole-bound state.  相似文献   

19.
Adiabatic and vertical ionization potentials (IPs) and valence electron affinities (EAs) of serinamide in the gas phase have been determined using density functional theory (DFT) B3LYP, B3P86, and B3PW91 methods with the 6‐311++G** and 6‐311G** basis sets, respectively. IPs and EAs of serinamide in solution have been calculated with the B3LYP method using the 6‐311++G** and 6‐311G** basis sets. Eight possible conformers of serinamide and its charged states in the gas phase have been optimized employing the DFT B3LYP method with 6‐311++G** and 6‐311G** basis sets, respectively. All the adiabatic and vertical ionization potentials (AIPs and VIPs) of eight serinamide conformers in our work are positive values, whether in the gas phase or in solutions; the IPs in solutions are smaller than the results in the gas phase and decrease with increased dielectric constants in solutions. This finding indicates that the cationic states in solutions are more stable than those in the gas phase. All EAs of eight serinamide conformers are negative values in the gas phase, indicating that the anionic states are unstable with respect to electron autodetachment, both adiabatically and vertically. In contrast, all other adiabatic electron affinities (AEAs) are negative values in solutions except for 6S in water; 7S in chloroform, acetone, and water; and 8S in acetone and water, and increase with increasing of dielectric constants in solutions. All vertical electron affinities (VEAs) are negative values in solutions; however, no good rule has been found for these values in solutions. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006  相似文献   

20.
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