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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.
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
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5.
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
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7.
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
8.
Eight H-bonded complexes between isocytosine (isoC) tautomeric forms and R/S-lactic acid (LA) have been studied at the B3LYP and HF levels of theory using 6–31+G(d) basis set. The energy barriers of the intermolecular proton transfers were also estimated as the results showed that they are several times lower than those of the intramolecular proton transfers of isoC in the gas phase. Furthermore, the energy barriers of the tautomerizations in which the carboxylic H-atom takes part are several times lower than those in which the LA OH group assists the proton transfer.
Figure 相似文献
9.
The adsorption and primary oxidation step for the photodegradation of nitrobenzene (NB) have been studied computationally
using MSINDO SCF MO method. The method performs efficiently for extended surface models such as Ti36O90H36. Molecular dynamics simulations have revealed that NB is linked to TiO2 surface at the titanium ion via the oxygen atoms of NO2 group. In addition, the computed vibrational density of states for the adsorbed NB molecule is in reasonably good agreement
with the available experimental data and theoretical results. In order to identify the primary photochemical and photocatalytic
•OH initiated photooxidation intermediates, we have employed two different theoretical approaches, frontier orbital theory
and Wheland localization theory. It has been found that the meta- hydroxynitrocyclohexadienyl radical is energetically more favored than para- and ortho-hydroxynitrocyclohexadienyl radicals for the photochemical photolysis, whereas in the case of photocatalysis, the •OH radical attack is unselective and all three possible isomers have comparable stabilities.
Figure Minimum energy adsorption conformation of nitrobenzene onto TiO2 (100) surface 相似文献
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Recently, our research group has proposed the hydroxyfurazanyl (4-hydroxy-1,2,5-oxadiazole-3-yl) moiety as a new non-classical
isoster of the carboxy function in the design of γ-aminobutyric acid (GABA) analogues. Some compounds showed significant activity
at the GABAA receptor, representing the only examples of pentatomic heterocycles bearing an ω-aminoalkyl flexible side chain in the position
vicinal to the hydroxy group displaying agonist activity at this receptor subtype. In this work, an ab initio analysis of the structural and electronic features of furazan-3-ol is presented, in order to provide a theoretical basis
to the claimed bioisosterism with the carboxy function. An ab initio conformational study with the C-PCM implicit solvent model was carried out to elucidate the reasons of the peculiar behaviour
of the furazan models. Alongside, another conformational search through molecular dynamics in explicit solvent was accomplished,
in order to validate the first method. The electronic features of the 4-hydroxy-1,2,5-oxadiazole-3-yl substructure seem to
account for a marked stabilising effect of the putative bioactive conformation at the GABAA receptor subtype. The 1,2,5-thiadiazole analogue, which shares the same conformational preference of its oxygenated counterpart,
was identified as a potential candidate for synthesis and pharmacological testing.
Figure 4-(ω-aminoalkyl)-1,2,5-oxadiazole-3-ol analogues of GABA
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorised users. 相似文献
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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.
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14.
The two possible routes to synthesize poly (lactic acid) are polycondensation of the lactic acid and ring opening polymerization
(ROP) of the lactide. This work involves molecular modeling of the polymerization initiation mechanisms using different initiators
a) H2SO4 for polycondensation b) aluminum isopropoxide for coordination-insertion ROP c)methyl triflate for cationic ROP, and d) potassium
methoxide for anionic ROP. For molecular modeling of PLA, we have benchmarked our approach using Ryner’s work on ROP of L-lactide
using stannous (II) 2-ethylhexanoate (Sn(Oct)2) and methanol as initiators. Our values of -15.2 kcal mol-1 and -14.1 kcal mol-1 for enthalpy changes in the two steps of activated complex formation match with Ryner’s. Geometric and frequency optimizations
have been done on Gaussian’03 using B3LYP density functional theory along with the basis sets LANL2DZ for metal atoms and
6–31G* and 6–31G** for non metal atoms. The kinetic rate constant for each mechanism has been calculated using the values of energy of activation, change in enthalpy, Gibbs free energy, entropy
and the partition functions from the Gaussian’03 output. Our polycondensation rate constant value of 1.07 × 10–4 se-1 compares well with 1.51 × 10–4 se-1 as reported by Wang. However, ROP rate constants could not be validated due to lack of experimental data.
Figure Cationic Ring Opening Polymerization of L-Lactide
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15.
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
16.
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
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18.
Marek Doskocz Agnieszka Strupińska Szczepan Roszak Monika Prokopowicz Leo H. Koole Paweł Kafarski 《Journal of molecular modeling》2009,15(6):651-658
The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes.
The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH2OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the 4h
J
NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models.
Figure Coupling constants in 8-bromo-2′,3′-O-isopropylideneadenosine
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
19.
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