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1.
A systematic study on the geometric structures, relative stabilities, and electronic properties of small bimetallic Au
n
Na (n = 1-9) clusters has been performed by means of first-principle density functional theory calculations at the PW91PW91 level.
The results show that the optimized ground-state isomers adopt planar structures up to n = 5, and the Na-capped geometries are dominant growth patterns for n = 6-9. Dramatic odd-even alternative behaviors are obtained in the second-order difference of energies, fragmentation energies,
highest occupied-lowest unoccupied molecular orbital energy gaps, and chemical hardness for both Au
n
Na and Au
n+1 clusters. It is found that Au5Na and Au6 have the most enhanced stability. Here, the size evolutions of the theoretical ionization potentials are in agreement with
available experimental data, suggesting a good prediction of the lowest energy structures in the present study. In addition,
the charge transfer has been analyzed on the basis of natural population analysis. 相似文献
2.
Rza Abbasoglu 《Journal of molecular modeling》2010,16(4):781-788
The geometry and electronic structure of exo-tricyclo[3.2.1.02,4]oct-6-ene (exo-TCO) was investigated using DFT methods. The two faces of the endo-pyramidalised double bond of the molecule
are not equivalent. The exo face of the double bond has regions with high electron density (q
i,HOMO) and greater negative potential. Molecular complexes of exo-TCO with bromine were investigated using the B3LYP/6-311++G(d,p)
method; the exo-TCO . . . Br2(exo) molecular complex was found to be relatively more stable than the exo-TCO . . . Br2(endo) complex. The cationic intermediates of the reaction were studied by DFT and MP2 methods. The solvent effect was evaluated
using the self-consistent isodensity polarised continuum model (SCI-PCM). The exo-bromonium cation was found to be more stable
than the endo-bromonium cation. Exo-facial selectivity due to electronic and steric factors was observed upon addition of
bromine to exo-TCO. The multicentre nonclassical delocalised bromocarbonium cation IV and the exo-bridged-bromonium cation I are more stable than the rearrangement cation V. The reaction products are formed via exo-bridged-bromonium I and nonclassical IV cations, which are the most stable intermediates and whose stabilities barely differ. The mechanism of the addition reaction
is also discussed. 相似文献
3.
Bárbara Herrera Francisco Gracia Paulo Araya Alejandro Toro-Labbé 《Journal of molecular modeling》2009,15(4):405-410
A theoretical study on (ZrO2)
n
(n = 1–5) and Cu/ZrO2 oligomers is presented, DFT/B3LYP/6-31G** calculations along with Lanl2DZ pseudopotentials on metallic centers have been
used to predict ionization potentials and electron affinities, chemical potentials and bandgaps indicating that the reactivity
reaches reasonably constant values at n = 5. The effect of copper atoms adsorbed on (ZrO2)
n
is discussed and the reactivity of oligomers of ZrO2 and Cu/ZrO2 are compared, results indicate that Cu activates the systems by localizing the specific nucleophilic and electrophilic reactivity. 相似文献
4.
A series of crown ethers containing the azobenzene moiety incorporated into crowns of various sizes [Cr(O6), Cr(O7) and Cr(O8)] and their corresponding alkali metal cation (Li+, Na+, K+, Rb+) complexes have been studied theoretically. The density functional theory (DFT) method was employed to elucidate the stereochemical
structural natures and thermodynamic properties of all of the target molecules at the B3LYP/6-31 G(d) and LANL2DZ level for
the cation Rb+. The fully optimized geometries had real frequencies, thus indicating their minimum-energy status. In addition, the bond
lengths between the metal cation and oxygen atoms, atomic torsion angles and thermodynamic energies for complexes were studied.
Natural bond orbital (NBO) analysis was used to explore the origin of the internal forces and the intermolecular interactions
for the metal complexes. The calculated results show that the most significant interaction is that between the lone pair electrons
of electron-donating oxygens in the cis-forms of azobenzene crown ethers (cis-ACEs) and the LP* (1-center valence antibond lone pair) orbitals of the alkali-metal cations (Li+, Na+, K+ and Rb+). The electronic spectra for the cis-ACEs [cis-Cr(O6), cis-Cr(O7) and cis-Cr(O8)] are obtained by the time-dependent density functional theory (TDDFT) at the B3LYP/6-31 G(d) level. The spectra of the cis-isomers show broad π → π* (S0 → S2) absorption bands at 310–340 nm but weaker n → π* (S0 → S1) bands at 480–490 nm. The calculated results are in good agreement with the experimental results. 相似文献
5.
Atle Wibe Anna-Karin Borg-Karlson Torbjörn Norin Hanna Mustaparta 《Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology》1997,180(6):585-595
Naturally produced plant volatiles, eliciting responses of single olfactory receptor neurons in the pine weevil, have been
identified by gas chromatography linked with mass spectrometry. The receptor neurons (n = 72) were classified in 30 types, according to the compound which elicited the strongest response in each neuron, 20 of
which compounds were identified. Most potent for 14 types of neurons (n = 50) were monoterpenes, including bicyclic (e.g. α-pinene, camphor and myrtenal) for 8 types (n = 32), monocyclic (limonene, carvone, α-terpinene) for 3 types (n = 12) and acyclic (e.g. β-myrcene and linalool) for 3 types (n = 6). Other compounds eliciting strongest responses of a neuron were five sesquiterpenes, including α-copaene and a farnesene-isomer,
and an anethole type which has no biosynthetic relationship with terpenes. Within one type, receptor neurons with quite selective
responses to the most potent compound as well as neurons with additional responses to several, structurally similar compounds
were found, indicating that the neurons may have the same functional types of membrane receptors, but different sensitivities.
Response spectra of neurons within the bicyclic-, mono-cyclic and acyclic types showed more overlapping than across the neuron
types. Minimal overlapping response spectra was found between monoterpene and sesquiterpene neurons. The results suggest that
this structure-activity relationship is significant for encoding plant odour information in the pipe weevil.
Accepted: 6 January 1997 相似文献
6.
Andruniów T 《Journal of molecular modeling》2007,13(6-7):775-783
Resonance Raman (RR) spectra of green fluorescent protein (GFP) model chromophores in solution have been simulated with the
CASSCF/MM methodology. Although several reports on vibrational analysis of GFP model chromophores have been recently published,
the RR spectra were simulated for the first time in explicit solution with the inclusion of the counterion, as these effects are crucial for unambiguously reproducing the vibrational
band assignment in the anionic form of the GFP chromophore. This strategy allows for a one-to-one correspondence of the calculated
vibrational modes to the observed RR bands, concerning both the location and intensity pattern. In addition, these simulations
were complemented with total energy distribution calculations to aid in the unambiguous assignment of the measured spectra.
The current study helps to clarify some of the previous RR bands assignments as well as producing some new assignment for
the anionic form of GFP chromophore. The explicit solvent simulations and PCM-based calculations are compared to the measured spectra, and these results demonstrate that explicit solvent simulations provide better agreement with experiment, both in terms of vibrational frequencies and intensity distribution.
Figure
a Correlation of explicit hydration calculations (CASSCF/6-31G*/MM) for the HBI model chromophore and experimental RR data [21]; slope = 0.982, intercept = 27.210 and regression coefficient = 0.997. b Correlation of implicit PCM calculations (CASSCF/6-31G*) for the HBI model chromophore and experimental RR data [21], slope = 1.017, intercept = −48.838 and regression coefficient = 0.984 相似文献
7.
Glasses in the system xGd2O3·(100-x)[GeO2·V2O5] with 0 ≤ × ≤ 20 mol% have been prepared from the melt quenching method. In this paper, we investigated changes in germanium
coordination number in gadolinium-vanadate-germanate glasses through molar volume analysis, measurements of densities, investigations
of FTIR and UV-VIS spectroscopy, calculations of density functional theory (DFT). Analyzing the structural changes resulted
from the IR spectra we found that the gadolinium ions have a pronounced affinity toward [VO4] structural units which contain non-bridging oxygens necessary for the charge compensation. The introduction of the excess
of oxygen yields the formation of [VO5] structural units. This attains maximum value at 5 mol% Gd2O3, in agreement with the density measurements. Further, the addition of the surplus of oxygen implies the transformation of
[VO5] to [VO4] structural units and the formation of VO4−3 orthovanadate structural units. The UV-VIS spectra show a broad UV absorption band located in the 300–500 nm region. These
bands are assumed to originate from the combination of vanadium ions possibly present in the three states of valence. The
presence of Ge-Ge wrong bonds attains its maximum values in the samples with x = 5 and 15 mol% Gd2O3 (bands centered in the 250–300 nm range). DFT calculations show the massive vibrations of the [VOn] structural units coupled with each other via [GeO6] and [GeO4] structural units. This leads to the splitting of the bridge modes and a multiplication of the number of these bands. 相似文献
8.
Daniela Josa Angeles Peña-Gallego Jesús Rodríguez-Otero Enrique M. Cabaleiro-Lago 《Journal of molecular modeling》2011,17(6):1267-1272
A comprehensive MP2/6-311 + G(d,p) and B3LYP/6-311 + G(d,p) study of the aromatic character of phospholes, P
n
(CH)4-n
PH with n = 0-4 was conducted. For this purpose, the structures for these compounds were optimized at both theoretical levels and different
magnetic properties (magnetic susceptibility anisotropy, χanis, and the nucleus-independent chemical shifts, NICS) were evaluated. For comparison, these magnetic properties were also calculated
in the optimized structures with planarity constraints. We have also applied the ACID (anisotropy of the current-induced density)
method in this analysis. The main conclusions are the aromatic character of these compounds, the relationship between aromaticity
and planarity and the importance of other factors in this aromaticity. 相似文献
9.
The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory
(DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond)
interaction characteristics in TA-(H2O)n (n = 1–3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are
retained in most TA-(H2O)n (n = 1–3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1–3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of
the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA.
Therefore, the most stable TA-(H2O)3 complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major
contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies
make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to
be significant. 相似文献
10.
The local meta-GGA exchange correlation density functional (TPSS) with a relativistic effective core potential was employed
to systematically investigate the geometric structures, stabilities, and electronic properties of bimetallic Ca2Au
n
(n = 1–9) and pure gold Au
n
(n ≤ 11) clusters. The optimized geometries show that the most stable isomers for Ca2Au
n
clusters have 3D structure when n > 2, and that one Au atom capping the Ca2Au
n−1 structure for different-sized Ca2Au
n
(n = 1–9) clusters is the dominant growth pattern. The average atomic binding energies and second-order difference in energies
show that the Ca2Au4 isomer is the most stable among the Ca2Au
n
clusters. The same pronounced even–odd alternations are found in the HOMO–LUMO gaps, VIPs, and hardnesses. The polarizabilities
of the Ca2Au
n
clusters show an obvious local minimum at n = 4. Moreover, the inverse corrections to the polarizabilities versus the ionization potential and hardness were found for
the gold clusters. 相似文献
11.
Serkan Demir Zuhal Yolcu Ömer Andaç Orhan Büyükgüngör Turan K. Yazıcılar 《Journal of molecular modeling》2010,16(9):1509-1518
A dinuclear centrosymmetric copper(II) complex with the formula [Cu2(μ-maa)4(maaH)2] has been synthesized and experimentally characterized by IR, electronic spectroscopy, and X-ray single-crystal diffractometry.
Starting from experimental X-ray geometry and using antiferromagnetic singlet ground state, gas phase geometry optimization
was performed by density functional hybrid (B3LYP) method with 6-31G(d) and LANL2DZ basis sets. Gas-phase vibrational frequencies
and single point energy (SPE) calculations have been carried out at the geometry-optimized structure. Molecular electrostatic
potential calculated at the optimized geometry and natural bond orbital analysis data have been extracted from SPE output.
The gas-phase electronic transitions of the title complex were investigated by the time dependent-density functional theory
(TD-DFT) approach with the same theory employing LANL2DZ basis set. Also the calculated UV-Vis based upon TD-DFT results and
IR spectra were simulated for comparison with the experimental ones. 相似文献
12.
The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Br2GaN3)
n
(n = 1–4) were studied at the B3LYP/6-311+G* level. The optimized clusters (Br2GaN3)
n
(n = 2–4) were all found to possess a cyclic structure consisting of Ga atoms bridged by the α-nitrogen of the azide groups.
A discussion of the relationships between the geometrical parameters and the degree of oligomerization n is provided. Features in the IR spectra were assigned by vibrational analysis. Trends in thermodynamic properties with temperature
and degree of oligomerization n are discussed. Thermodynamic analysis of the gas-phase reaction showed that the formation of the clusters (Br2GaN3)
n
(n = 2–4) is thermodynamically favorable considering the enthalpies at 298.2 K. The calculated results for the Gibbs free energies
were negative, which indicates that the oligomerizations can occur spontaneously at 298.2 K. 相似文献
13.
Ab initio methods based on density functional theory at BP86 level were applied to the study of the geometrical structures,
relative stabilities, and electronic properties of small bimetallic Be2Au
n
(n = 1–9) clusters. The optimized geometries reveal that the most stable isomers have 3D structures at n = 3, 5, 7, 8, and 9. Here, the relative stabilities were investigated in terms of the averaged atomic binding energies, fragmentation
energies and second-order difference of energies. The results show that the planar Be2Au4 structure is the most stable structure for Be2Au
n
clusters. The HOMO−LUMO gap, vertical ionization potential, vertical electron affinity and chemical hardness exhibit a pronounced
even–odd alternating phenomenon. In addition, charge transfer and natural electron configuration were analyzed and compared. 相似文献
14.
Bandyopadhyay D 《Journal of molecular modeling》2012,18(2):737-749
The present study reports the effect of oxygen addition on small size Nin (n = 1-6) clusters in different spin states within the framework of linear combination of atomic orbital (LCAO) density functional
theory (DFT) under spin polarized generalized gradient approximation (GGA) functional. Relative stabilities of the optimized
clusters are discussed on the basis of the calculated parameters, such as, binding energy (BE), embedding energy (EE) and
fragmentation energy (FE). Other parameters, like ionization potential (IP), electron affinity (EA), etc. show that though
the additions of oxygen can affect the chemical properties of Nin clusters with an additional stability to NinO. In most of the cases the magnetic moment of the stable isomers are geometry dependent for a particular size both in pure
and oxidized clusters. Calculated magnetic moments of NinO (n = 1-6) clusters reveal that the magnetic moment of ground state Ni4O isomers in different geometries is same as in pure Ni4 isomers. Present study also explains the cause of stable magnetic moment in Ni4O cluster through the distribution of electrons in different orbitals. 相似文献
15.
A theoretical study of L-proline-nH2O (n = 1–3) has been performed using the hybrid DFT-B3LYP and MP2 methods together with the 6-311++G(d,p) basis set. The results
show that the P2 conformer is energetically favorable when forming a hydrated structure, and the hydration of the carboxyl
group leads to the greatest stability. For hydrated complexes, the adiabatic and vertical singlet–triplet excitation energies
tend to decrease with the addition of water molecules. The hydration energy indicates that in the hydrated complexes the order
of stability is: binding site 2 > binding site 1 > binding site 3, and binding site 12 > binding site 23 > binding site 13.
As water molecules are added, the stabilities of these hydrated structures gradually increase. In addition, an infrared frequency
analysis indicated that there are some differences in the low-frequency range, which are mainly dominated by the O–H stretching
or bending vibrations of different water molecules. All of these results should aid our understanding of molecular behavior
and provide reference data for further studies of biological systems. 相似文献
16.
Photodimerization reactions of compounds 4–6 gave four new cyclobutane-containing compounds (7–9) with full control over the stereochemistry at the four stereogenic centers. These new cyclobutane-containing compounds had
β-truxinic (7a), δ-truxinic (7b and 9), and ε-truxillic (8) structures. However, o-, m-, and p-hydroxy 4-azachalcones (1–3) did not give photochemical cyclization products under any conditions (in solvent or in their solid or molten states). Experimental
data suggested the possibility of frontier orbital control over stereochemical behavior, so some theoretical calculations
were performed. Full geometrical optimization of compounds 1–9 was performed via DFT B3LYP/6-31+G**, and their electronic structures were also investigated. The geometries of the singlet and triplet states were initially
optimized by density functional theory (DFT) and the configuration interaction singles (CIS) B3LYP/3-21+G** level. An additional calculation was performed for the triplet state using the ground-state geometry. The possible photochemical
dimerization products of compounds 7–9 (a–g) and the intrinsic reaction coordinates (IRCs) of the reactions of compounds 4–6 were calculated theoretically by the DFT/3-21+G** method. The configurations (reactant, transition state, product, and reaction pathway) corresponding to the stationary
points (minima or saddle points) were determined. The intrinsic reaction coordinates were followed to verify the energy profiles
that connect each TS to the appropriate local minimum. The dimeric products expected from the calculations coincided with
the dimers produced experimentally. 相似文献
17.
Pradeep Risikrishna Varadwaj 《Journal of molecular modeling》2010,16(5):965-974
Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ
and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN···HX (X = F, Cl, Br) to examine the
variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics
in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent
monomers. The interaction energy (ΔE) calculated using a super-molecular model is found to be in this order: PN···HF > PN···HCl
> PN···HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma
(KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic
energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Δμ) was observed in these
complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN···HF > PN···HCl
> PN···HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in
this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic
blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological
or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify
and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond
formation. It is found from the analysis of the electron density ρ
c
, the Laplacian of electron charge density ∇2ρc, and the total energy density (H
c
) at the critical points between the interatomic regions that the interaction N···H is indeed electrostatic in origin (ρc > 0, ∇2ρc > 0 and Hc > 0 at the BCP) whilst the bonds in PN (ρc > 0, ∇2ρc > 0 and Hc < 0) and HX ((ρc > 0, ∇2ρc < 0 and Hc < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering,
E(2), caused by charge transfer mechanism shows that the interaction N···H is n(N) → BD*(HX) delocalization. 相似文献
18.
Machado NF Calheiros R Fiuza SM Borges F Gaspar A Garrido J Marques MP 《Journal of molecular modeling》2007,13(8):865-877
The conformational preferences of several potential anticancer dihydroxycinnamic esters with a variable length alkyl chain
were studied by quantum-mechanical (DFT) calculations (both for the isolated molecule and for aqueous solutions). The orientation
of the hydroxyl ring substituents and of the alkyl ester moiety relative to the carbonyl group showed these to be the most
determinant factors for the overall stability of this type of phenolic systems, strongly dependent on an effective π-electron
delocalization. Compared to the parent caffeic acid (dihydroxycinnamic acid), esterification was found to lead to a higher
conformational freedom, and to affect mainly the energy barrier corresponding to the (O=)C-OR internal rotation. No particular
differences were verified to occur upon lengthening of the ester alkyl chain, except when this is branched instead of linear.
The vibrational spectra of the whole series of compounds were simulated, based on their calculated harmonic vibrational frequencies,
and a preliminary assignment was performed.
Figure Schematic representation of the dihydroxycinnamic esters studied in the present work and of the main internal rotations affecting
the overall stability of the molecules. (R=(CH2)n, n = 0,1,2,3,7,11 for MC, EC, PC, BC, OC and DC, respectively; R=(CHCH3) for IPC. The atom numbering is included, with the exception of the alkyl ester group) 相似文献
19.
The Schiff base compound, 2-[(4-Fluorophenylimino)methyl]-3,5-dimethoxyphenol, has been synthesized and characterized by IR,
electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound
in the ground state have been compared using the Hartree-Fock (HF) and density functional method (B3LYP) with 6–31G(d) basis
set. Calculated results show that density functional theory (DFT) and HF can well reproduce the structure of the title compound.
The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6–31G(d) basis
set by applying the polarizable continuum model (PCM). The total energy of the title compound decrease with the increasing
polarity of the solvent. By using TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been
predicted and a good agreement with the TD-DFT method and the experimental ones is determined. In addition, DFT calculations
of the title compound, molecular electrostatic potential (MEP), natural bond orbital (NBO), and thermodynamic properties were
performed at B3LYP/6–31G(d) level of theory. 相似文献
20.
Eriksson C Frängsmyr L Danielsson Niemi L Loimaranta V Holmskov U Bergman T Leffler H Jenkinson HF Strömberg N 《Glycoconjugate journal》2007,24(2-3):131-142
Glycoprotein gp-340 aggregates bacteria in saliva as part of innate defence at mucosal surfaces. We have detected size- and
glycoforms of gp-340 between human saliva samples (n = 7) and lung gp-340 from a proteinosis patient using antibodies and lectins in Western blots and ELISA measurements. Western
blots of saliva samples, and of gp-340 purified, from the seven donors using a gp-340 specific antibody distinguished four
gp-340 size variants, designated I to IV (n = 2,2,2 and 1). While saliva gp-340 variants I to III had single bands of increasing sizes, variant IV and lung gp-340 had
double bands. Purified I to IV proteins all revealed a N-terminal sequence TGGWIP upon Edman degradation. Moreover, purified
gp-340 from the seven donors and lung gp-340 shared N-glycans, sialylated Galβ1-3GalNAc and (poly)lactosamine structures.
However, the larger size gp-340 grouping II/III (n = 4) and smaller size grouping I/IV correlated with a secretor, Se(+), and a non secretor, Se(−), dependent glycoform of
gp-340, respectively (p = 0.03). The Se(+) glycoforms contained ABH, Leb, Ley and polylactosamine structures, while the Se(−) glycoforms lacked ABH antigens but expressed Lea, Lex and lactosamine structures. By contrast, lung gp-340 completely lacked ABH, Lea/b, Lex/y or sLex structures. Gp-340 and secretor typing of saliva from additional donors (n = 29) showed gp-340 glycoforms I to IV for 6, 16, 4 and 0 donors, respectively, and 3 non-typeable donors, and verified that
gp-340 glycoforms I and II/III correlate with Se(−) and Se(+) phenotypes, respectively (p < 0.0001). The glycoforms of saliva and lung gp-340 mediated differential aggregation of Leb- (Helicobacter pylori), sialylpolylactosamine- (Streptococcus suis) or sialic acid- (Streptococcus mutans) binding bacteria. In conclusion, variant size- and glycoforms of gp-340 are expressed by different individuals and may modulate
the biological properties of gp-340 pertinent to health and disease. 相似文献