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1.
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
2.
3.
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
4.
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
5.
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
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Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane’s unsaturated
analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies
of combustion, specific enthalpies of combustion, and proton affinities. Our results indicate that the cis form of triazene
has a specific enthalpy of combustion of −15.2 kJ g−1 and the trans form has a specific enthalpy of combustion of −14.7 kJ g−1.
Figure Structures of cis- and trans-triazane, N3H3 相似文献
8.
Lee JY Doddareddy MR Cho YS Choo H Koh HY Kang JH No KT Pae AN 《Journal of molecular modeling》2007,13(5):543-558
Comparative quantitative structure–activity relationship (QSAR) analyses of peptide deformylase (PDF) inhibitors were performed
with a series of previously published (British Biotech Pharmaceuticals, Oxford, UK) reverse hydroxamate derivatives having
antibacterial activity against Escherichia coli PDF, using 2D and 3D QSAR methods, comparative molecular field analysis (CoMFA), comparative molecular similarity indices
analysis (CoMSIA), and hologram QSAR (HQSAR). Statistically reliable models with good predictive power were generated from
all three methods (CoMFA r
2 = 0.957, q
2 = 0.569; CoMSIA r
2 = 0.924, q
2 = 0.520; HQSAR r
2 = 0.860, q
2 = 0.578). The predictive capability of these models was validated by a set of compounds that were not included in the training
set. The models based on CoMFA and CoMSIA gave satisfactory predictive r
2 values of 0.687 and 0.505, respectively. The model derived from the HQSAR method showed a low predictability of 0.178 for
the test set. In this study, 3D prediction models showed better predictive power than 2D models for the test set. This might
be because 3D information is more important in the case of datasets containing compounds with similar skeletons. Superimposition
of CoMFA contour maps in the active site of the PDF crystal structure showed a meaningful correlation between receptor–ligand
binding and biological activity. The final QSAR models, along with information gathered from 3D contour and 2D contribution
maps, could be useful for the design of novel active inhibitors of PDF.
Figure Superimposition of comparative molecular field analysis (CoMFA) contour plot in the active site of peptide deformylase (PDF) 相似文献
9.
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
10.
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
11.
The molecular dynamics as well as ab initio MP2/6-31G(d = 0.25) single point calculations were performed for native and oxidized B-DNA telomeric fragments. The structural,
dynamic, energetic and electrostatic properties along with frontier orbitals distribution were described for the central triad
consisting of three guanine molecules in its canonical or oxidized forms. Although the average structural parameters characterizing
all of the studied telomere fragments are close each to other, the significant consequence on angular and displacement flexibilities
are observed. Namely, the increase of mutual displacement of two successive base pairs along either axis and increase of the
rotation of two bases of opposite strand are main dynamic consequences of presence of 8-oxo-guanine in the central triad of
telomeric B-DNA. Besides, the significant increase of stacking energies in case of 8-oxo-guanine were found. Furthermore,
the guanine pattern visible from the major groove may be described as donor-acceptor-acceptor formed by H8-N7-O6 atoms, respectively. To the contrary the presence of 8-oxo-guanine changes the electrostatic properties of the major groove
into acceptor-donor-acceptor coming from O8-H7-O6 atoms. This results in significant alteration of ESP characteristics. Finally, the molecular orbital properties are also
significantly affected by oxidation of telomeric B-DNA fragments. All these factors contribute to decrease of binding of telomere
proteins.
Figure The consequences of guanine oxidation in central GGG telomeric triad on electrostatic properties of CCGTACTT-A1G2G3G4T5T6-AGGGTT-AACA telomere fragment
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
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Pharmacophore mapping studies were undertaken for a series of molecules belonging to pyrrolopyrimidines, indolopyrimidines
and their congeners as multidrug resistance-associated protein (MRP1) modulators. A five-point pharmacophore with two hydrogen
bond acceptors (A), one lipophilic/hydrophobic group (H), one positive ionic feature (P) and one aromatic ring (R) as pharmacophoric
features was developed. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a correlation
coefficient of r
2 = 0.799 for training set molecules. The model generated showed excellent predictive power, with a correlation coefficient Q
2 = 0.679 for an external test set of 20 molecules. The pharmacophore was further validated using four structurally diverse
compounds with MRP1 modulatory activity. These compounds mapped well onto four of the five features of the pharmacophore.
The pharmacophore proposed here was then utilised for the successful retrieval of active molecules with diverse chemotypes
from database search. The geometry and features of pharmacophore are expected to be useful for the design of selective MRP1
inhibitors.
Figure Alignment of multidrug resistance-associated protein (MRP1) inhibitors with the developed pharmacophore.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
15.
Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied
at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of
the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the
calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton
transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999).
Figure H-bonded complex between i-propanol and adenine 相似文献
16.
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
17.
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
18.
The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated
in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the
complex, in which the interacting site is a C≡N and C=C bond center in the TCNE and, –NH2 and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy,
estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the
reported experimental value in chloroform medium.
TCNE-aniline at ground state. TCNE-aniline at excited state 相似文献
19.
Cyclin-dependent kinases (Cdks) play important roles in the regulation of the cell cycle. Their inhibitors have entered clinical
trials to treat cancer. Very recently, Davis et al. (Nat Struct Biol 9:745–749, 2002) have found a ligand NU6102, which has
a high affinity with cyclin-dependent kinase 2 (K
i
=6 nM) but a low affinity with cyclin-dependent kinase 4 (K
i
=1,600 nM). To understand the selectivity, we use homology modeling, molecular docking, molecular dynamics and free-energy
calculations to analyze the interactions. A rational 3D model of the Cdk4–NU6102 complex is built. Asp86 is a key residue
that recognizes NU6102 more effectively with Cdk2 rather than Cdk4. Good binding free energies are obtained. Energetic analysis
reveals that van der Waals interaction and nonpolar contributions to solvent are favorable in the formation of complexes and
the sulfonamide group of the ligand plays a crucial role for binding selectivity between Cdk2 and Cdk4.
Figure Two-dimensional representative for the interacting model of NU6102 complexed with the Cdk4 from a predicted structure by
LIGPLOT.
相似文献
20.
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