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1.
As a follow-up study to our study on tetrazane (N4H6), we present computed thermodynamic properties of triazane (N3H5). Calculated properties include optimized geometries, infrared vibrations, enthalpy of formation, enthalpy of combustion,
and proton affinities. We have also mapped the potential energy surface as the molecule is rotated about the N-N bond. We
have predicted a specific enthalpy of combustion for triazane of about -20 kJ g−1.
Figure Schematic diagram of the dielectric barrier discharge (left) and typical temporal profiles of voltage and current, as obtained
from the simulations (right) 相似文献
2.
Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of
their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties
of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies,
enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate
that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about
−52 kJ per gram.
Figure Optimized geometry for R-azatriborospiropentane (10)
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
3.
The structure and stability of endohedral X@C20F20 complexes (X = H−, F−, Cl−, Br−, H, He) have been computed at the B3LYP level of theory. All complexes in I
h symmetry were found to be energy minimum structures. H−@C20F20 and F−@C20F20 complexes have negative inclusion energies, while other complexes have positive inclusion energies. Similarity between C20F20 and C20H20 has been found for X = H and He. On the basis of the computed nucleus independent chemical shift values at the cage center,
both C20F20 and C20F20 are aromatic.
Figure Endohedral X@C20F20 complexes 相似文献
4.
Stewart JJ 《Journal of molecular modeling》2007,13(12):1173-1213
Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization
are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed
70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for
4,492 species was 8.0 kcal mol−1. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal
mol−1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal
mol−1. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction
of geometries.
Figure Calculated structure of the complex ion [Ta6Cl12]2+ (footnote): Reference value in parenthesis
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
5.
Karhánek D Kacer P Kuzma M Splíchalová J Cervený L 《Journal of molecular modeling》2007,13(9):1009-1016
Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the
strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of
ethylene derivatives was evaluated in terms of the Pt-olefin binding energy using MP2 correlation theory. Organometallics
bearing coordinated olefins with general formula (R1R2C = CR3R4)Pt(PH3)2 [R = various substituents] had been selected, including olefins containing both electron-donor substituents as well as electron-withdrawing
groups. The stability of the corresponding complexes increases with a strengthening electron-withdrawal ability of the olefin
substituents.
Figure Representation of (CH2 = CHR)Pt(PPh3)2 and the stability chart 相似文献
6.
A series of [XN5]− (X=O, S, Se, Te) compounds has been examined with ab initio and Density Functional Theory (DFT) methods. The five-membered nitrogen ring series of structures are global minima and may exist or be characterized due to their significant dissociation barriers (29.7–32.7 kcal mol−1). Nucleus-independent chemical shifts (NICS) criteria and the presence of (4n+2) π-electrons confirmed that the five-membered nitrogen ring in their structures exhibits characteristics of aromaticity. Thus, the strong stability of the five-membered nitrogen ring structures may be attributed partially to their aromaticity.
相似文献
7.
49Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6–31G(d)//B3LYP/6–31G(d) proves to give very good agreement with experimental data over a range from 1,400 to −1,300 ppm. The MP2/6–31G(d)//MP2/6–31G(d) level computes even smaller average deviations but fails for TiI4. This behavior together with its huge demand for computational resources requires careful handling of this theoretical level. In addition, NMR data for five titanium fulvene (or related) complexes are given.
Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
8.
Setzer WN 《Journal of molecular modeling》2008,14(5):335-342
The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated
using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods
give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective
germacrenes (by around 3–4 kcal mol−1) and smaller activation energies (by 2–3 kcal mol−1). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently,
the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at
these levels of calculation.
Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone 相似文献
9.
An organic molecule, designed in this study, is proposed as a candidate molecular switch and characterized using the B3LYP/6-31G*
computational method. Structural and electronic properties of this molecular switch (M) and its singly charged (M+ and M−) species in their lowest and the first higher spin states are calculated and analyzed. Molecular volume and electronic spatial
extent (ESE) of this nanoswitch undergo negligibly small changes (<2%) upon charging. Furthermore, the small difference between
the calculated dipole moments of the M+ and M− species shows that switching between negative and positive poles does not significantly affect the charge transfer performance
of this molecular switch. Natural bond orbital (NBO) and spin density distributions are also calculated and analyzed. A preliminary
study on the response of the proposed molecular switch to the external electric field approves its function as a multi-pole
nanoswitch controlled by a bias voltage.
Figure Electron transfer scheme and arrangement of the π-electrons in the turn-on state of the candidate multi-pole molecular switch. 相似文献
10.
The ONIOM2 (B3LYP/6–31G (d, p): PM3) and B3LYP/6–31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found at B3LYP/6–31G (d, p) level to have hydrogen bonds and π....π stacking interaction,
their binding energy via HAF optimization was −20.4 kcal mol−1. The results derived from this study agreed well with the reported observation.
Figure Optimized structure of STI-571 and Thr315 in abelson tyrosine kinase based on ONIOM2 method 相似文献
11.
The structures and stabilities of square–hexagon alternant boron nitrides (B
x
N
x
, x=12–36) vs their tube isomers containing octagons, decagons and dodecagons have been computed at the B3LYP density functional level of theory with the correlation-consistent cc-pVDZ basis set of Dunning. It is found that octagonal B20N20 and B24N24 tube structures are more stable than their square–hexagon alternants by 18.6 and 2.4 kcal mol−1, respectively, while the square–hexagon alternants of other cages are more stable. Trends in stability as a function of cluster size are discussed.Figure The octagonal B20N20 and B24N24 tube structures are more stable than their square-hexagon alternant cagesDedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
12.
The thermal decomposition of model compounds for poly (dialkyl fumarate) was studied by using ab initio and density functional theory (DFT) calculations. To determine the most favorable reaction pathway of thermal decomposition,
geometries, structures, and energies were evaluated for reactants, products, and transition states of the proposed pathways
at the HF/6-31G(d) and B3LYP/6-31G(d) levels. Three possible paths (I, II and III) and subsequent reaction paths (IV and V)
for the model compounds of poly (dialkyl fumarate) decomposition had been postulated. It has been found that the path (I)
has the lowest activation energy 193.8 kJ mol−1 at B3LYP/6-31G(d) level and the path (I) is considered as the main path for the thermal decomposition of model compounds
for poly (dialkyl fumarate).
相似文献
13.
Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are
modified to simulate the catalyzed growth of single-wall carbon nanotubes on Nin clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of
the metal atoms on such interactions.
Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters. 相似文献
14.
A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)—pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20–25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH–O and one CH–O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of −41.2 kcal mol−1 at the BHandHLYP/6-311++G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol−1, giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes.
Figure
Formation of DB24C8-DBM pseudorotoxane complex 相似文献
15.
3D-QSAR and molecular docking analysis were performed to explore the interaction of estrogen receptors (ERα and ERβ) with
a series of 3-arylquinazolinethione derivatives. Using the conformations of these compounds revealed by molecular docking,
CoMFA analysis resulted in the first quantitative structure-activity relationship (QSAR) and first quantitative structure-selectivity
relationship (QSSR) models predicting the inhibitory activity against ERβ and the selectivity against ERá. The q2 and R2 values, along with further testing, indicate that the obtained 3D-QSAR and 3D-QSSR models will be valuable in predicting
both the inhibitory activity and selectivity of 3-arylquinazolinethione derivatives for these protein targets. A set of 3D
contour plots drawn based on the 3D-QSAR and 3D-QSSR models reveal modifications of substituents at C2 and C5 of the quinazoline
which my be useful to improve both the activity and selectivity of ERβ/ ERα. Results showed that both the steric and electrostatic
factors should appropriately be taken into account in future rational design and development of more active and more selective
ERβ inhibitors for the therapeutic treatment of osteoporosis.
Figure Structures of ERβ binding with compounds 1aar, 1ax and 1aag obtained from molecular docking 相似文献
16.
We present the results of simulations of a CCl4 monolayer adsorbed on a graphite surface. The CCl4 molecule was represented either by a shapeless superatom or by its atomic sites. The simulations were carried out over a
large range of temperatures, from 20 K up to 340 K. We address the following problems: (1) the influence of molecular shape
on the structure and stability of phases (particularly at low temperatures), and (2) the influence of the graphite corrugation
on layer stability and mechanism of phase transitions. In particular, we discuss the possibility and conditions of the appearance
of hexatic phase in the system.
Figure Temperature dependence of Φ6 order parameter for CCl4 monolayer adsorbed onsmooth and corrugated surfaces, in the spherical Lennard Jones (LJ) approximation.For comparison, the
order parameter calculated for MacDonald’s five-site potential is also presented 相似文献
17.
Tezer N 《Journal of molecular modeling》2008,14(1):11-20
The protomeric tautomerizm and conformation of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule were investigated,
and its three neutral tautomers (B1,B2,B3) and their rotamers (C1,C2,C3) were considered. Full geometry optimizations were carried out at the HF/6-31G* and B3LYP/6-31G* levels in gas phase and
in water. The tautomerization processes in water (ɛ = 78.54) were studied by using self-consistent reaction field theory.
The calculation showed that the boat conformation is dominant for the seven-membered diazepine ring in all of the structures,
even with different double bond positions. The calculated relative free energies (ΔG) showed that the tautomer C1 was the most stable structure, and its conformer B1 was the second most stable in the gas phase and in water.
Figure 2-Methyl-4-pyridin-2′-yl-1,5-benzodiazepine 相似文献
18.
In this paper, we proposed a new method for the determination of either human serum albumin (HSA) or 5-Aminosalicylic acid
(5-ASA) by synchronous fluorescence spectra and examined the interaction between them using the molecular modeling method
under simulative physiological conditions. The optimum conditions of synchronous fluorometric determination of HSA were investigated
and the method was successfully applied to the determination of 5-ASA added to serum, urine, and saliva samples. The linear
range of the determination of HSA and 5-ASA were 1.60 – 414 μg mL−1 and 0.76 –22.95 μg mL−1, the detection limits were 0.552 μg mL−1 and 0.38 μg mL−1, respectively. In addition, the effect of various common ions on the determination of HSA with 5-ASA was also discussed at
room temperature.
Figure The salicylic acid moiety is located within the binding pocket. The ring of 5-ASA was inserted in the hydrophobic cavity of
site I, and it is important to note that the residue ARG-218 and the trptophan residue of HSA (Trp214) are in close proximity
to the ring of 5-ASA suggesting the existence of hydrophobic interaction between them. 相似文献
19.
Nongnit Morakot Wandee Rakrai Somchai Keawwangchai Chatthai Kaewtong Banchob Wanno 《Journal of molecular modeling》2010,16(1):129-136
The thiourea based receptor containing naphthalene groups (1), has been successfully designed and synthesized for application as an oxalate receptor. A density functional theory at B3LYP/6-31G(d,p)
level of theory has been applied to predict the binding ability between 1 and selected anions, i.e., oxalate, malonate, succinate, glutarate, dihydrogen phosphate, and hydrogen sulphate. Calculation results point out that
receptor 1 shows the strongest interaction to oxalate ion with the binding free energy of 172.48 kcal mol−1. The recognition ability of 1 to the selected anions has been also investigated by means of the absorption and emission techniques. Experimental results
are in excellent agreement with the calculation data in which receptor 1 shows highly selective for oxalate ion over the other anions with logβ of 3.82 (0.02) M−1 by means of the size of binding cavity.
相似文献
20.
The possibility that stable complexes may be formed between alpha particles (He2+) and small molecules is investigated using QCISD quantum mechanical calculations. Implications for their presence in the
terrestrial atmosphere and/or in interstellar space are discussed.
Figure Optimized structure of a stable H2OHe2+ complex 相似文献