A theoretical study of a sandwich compound with a metal monolayer sheet between two aromatic ligands is presented. A full
geometry optimization of the [Au3Cl3Tr2]2+ (1) compound, which is a triangular gold(I) monolayer sheet capped by chlorines and bounded to two cycloheptatrienyl (Tr)
ligands was carried out using perturbation theory at the MP2 computational level and DFT. Compound (1) is in agreement with
the 18–electron rule, the bonding nature in the complex may be interpreted from the donation interaction coming from the Tr
rings to the Au array, and from the back-donation from the latter to the former. NICS calculations show a strong aromatic
character in the gold monolayer sheet and Tr ligands; calculations done with HOMA, also report the same aromatic behavior
on the cycloheptatrienyl fragments giving us an insight on the stability of (1). The Au –Au bond lengths indicate that an
intramolecular aurophilic interaction among the Au(I) cations plays an important role in the bonding of the central metal
sheet.
Figure (a) Ground state geometry of complex 1; (b) Top view of compound 1 and Wiberg bond orders computed with the MP2/B1 computational method; (c) Lateral view of compound 1 and NICS values calculated with the MP2/B1 method; the values in parenthesis were obtained at the VWN/TZP level 相似文献
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
Microsomal prostaglandin E2 synthase (mPGES-1) has been identified recently as a novel target for treating pain and inflammation. The aim of this study
is to understand the binding affinities of reported inhibitors for mPGES-1 and further to design potential new mPGES-1 inhibitors.
3D-QSAR-CoMFA (comparative molecular field analysis) and CoMSIA (comparative molecular similarity indices analysis) - techniques
were employed on a series of indole derivatives that act as selective mPGES-1 inhibitors. The lowest energy conformer of the
most active compound obtained from systematic conformational search was used as a template for the alignment of 32 compounds.
The models obtained were used to predict the activities of the test set of eight compounds, and the predicted values were
in good agreement with the experimental results. The 3D-QSAR models derived from the training set of 24 compounds were all
statistically significant (CoMFA; q2 = 0.89, r2 = 0.95, , and CoMSIA; q2 = 0.84, r2 = 0.93, , ). Contour plots generated for the CoMFA and CoMSIA models reveal useful clues for improving the activity of mPGES-1 inhibitors.
In particular, substitutions of an electronegative fluorine atom or a bulky hydrophilic phenoxy group at the meta or para positions of the biphenyl rings might improve inhibitory activity. A plausible binding mode between the ligands and mPGES-1
is also proposed. 相似文献
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
G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation
of oncogenes. In this study, molecular models were created for the c-MYC NHE-III1 (nuclease hypersensitivity element III1) from two 39-base complementary sequences. The NHE modeled here consists of single folded conformers of the polypurine intramolecular
G-Quadruplex and the polypyrimidine intramolecular i-Motif structures, flanked by short duplex DNA sequences. The G-Quadruplex
was based on published NMR structural data for the c-MYC 1:2:1 loop isomer. The i-Motif structure is theoretical (with five
cytosine–cytosine pairs), where the central intercalated cytosine core interactions are based on NMR structural data obtained
for a tetramolecular [d(A2C4)4] model i-Motif. The loop structures are in silico predictions of the c-MYC i-motif loops. The porphyrin meso-tetra(N-methyl-4-pyridyl)porphine
(TMPyP4), as well as the ortho and meta analogs TMPyP2 and TMPyP3, were docked to six different locations in the complete
c-MYC NHE. Comparisons are made for drug binding to the NHE and the isolated G-Quadruplex and i-Motif structures. NHE models
both with and without bound cationic porphyrin were simulated for 100 ps using molecular dynamics techniques, and the non-bonded
interaction energies between the DNA and porphyrins calculated for all of the docking interactions.
Figure Molecular models of the average structure of the final 20 ps of the molecular dynamics simulation of the c-MYC NHE-III1 (nuclease hypersensitivity element III1) “silencer” element. The G-Quadruplex structure is at the top-center, and the i-Motif is at the bottom-center of each picture.
a “Rotation #1” of the G-Quadruplex, with the T15 loop at the top and rear and the G19/A20 loop at the top and front of the picture. b “Rotation #2” of the G-Quadruplex, with the T15 loop at the top and front of the image, and the G19/A20 loop at the front and adjacent to the G-Quadruplex/i-Motif interface 相似文献
We have analyzed the electronic structure and chemical bonding for molecular adducts of the Ag(II)F2 molecule with various aza Lewis bases including ammonia, nitriles, secondary amines, and their derivatives exhibiting various
degrees of fluorination. Density functional theory calculations indicate that a progressive shift occurs of the spin density
from the Ag center towards the coordinating nitrogen atoms of aza ligands, as the ligation energy increases. Chemistry of
Ag(II) might be extended with little effort beyond the known aza connections, to include nitriles, perfluorinated nitriles
and perfluorinated amines.
Figure Properties of a variety of novel adducts of the AgF2 molecule with two aza bases (L), possible precursors of the AgF2L2 extended solids, were assessed by the DFT calculations
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
This work is dedicated to memory of Wojciech Ochmański, unforgettable person, good-hearted man, whose craftsmanship in work
was second-to-none. 相似文献
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
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
For the first time, the structures, stabilities and electronic properties of alkaline-earth metal doped B44 fullerenes were investigated by means of density functional theory calculations. Our results reveal that M@B44 (M = Ca, Sr, Ba) possess endohedral configurations as their lowest energy structures, whereas the exohedral form is favored when metal is Be or Mg. The large binding energies and sizable HOMO–LUMO gap energies of Ca@B44, Sr@B44 and Ba@B44 suggest the considerable possibility to achieve these novel endohedral borofullerenes experimentally. Born-Oppenheimer molecular dynamics (BO-MD) simulations at various temperatures further confirmed the extreme dynamic stabilities of these endohedral complexes. Their bonding patterns were also analyzed in detail. Finally, we simulated their infrared absorption spectra and 11B nuclear magnetic resonance spectra to help future structural characterization.
Structure-based 3D-QSAR studies were performed on 20 thiazoles against their binding affinities to the 5-HT3 receptor with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The thiazoles were initially docked into the binding pocket of a human 5-HT3A receptor homology model, constructed on the basis of the crystal structure of the snail acetylcholine binding protein (AChBP), using the GOLD program. The docked conformations were then extracted and used to build the 3D-QSAR models, with cross-validated values 0.785 and 0.744 for CoMFA and CoMSIA, respectively. An additional five molecules were used to validate the models further, giving satisfactory predictive values of 0.582 and 0.804 for CoMFA and CoMSIA, respectively. The results would be helpful for the discovery of new potent and selective 5-HT3 receptor antagonists.
相似文献
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 Ih 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
The 1A1 ground and the first 1B2 excited states of the methylenecyclopropene (triafulvene) are described by localized wave functions, based on 20 structures valence bond structures. The results are compared to CASSCF(4,4) calculations for both the energetics and the dipole moment. Additional calculations with partial electronic delocalization are presented, and it is shown that the dipole moment modification does not correspond to a situation where the antiaromatic situation prevails (with 4n electrons in the cycle). Part of the analysis uses a “trust factor” that helps to decide if a wave function is appropriate to describe a given state. The trust factor compares the VB wave function to the CASSCF’s with their overlap. Finally, the valence bond density is used to produce density maps that illustrate the electron transfer upon excitation.
Graphical Abstract A projector-based method compares CASSCF wave functions to local wave functions, including Lewis structures as shown in the picture. A “trust factor” (τ) is obtained. Both the ground state and the first excited state of the methylenecyclopropene are discussed
Density functional theory (B3LYP, B3LYP-D2 and wB97XD functionals) was used in finite models of zigzag carbon nanotubes (CNT), (n,0)×k with n?=?6–9 and k?=?2–4, to systematically investigate the effects of size on their structural and electronic properties. We found that the ratio between the length (Lt) and the diameter (dt) of the pristine CNT has to be larger than 2, i.e., Lt/dt?>?2, in order to provide the observed experimental trends of C=C bond distances, as well as to maintain the atomic charges nearly constant and zero around the center of the tube. Therefore, the concepts of useful length and volume were developed and tested for the encapsulation process of HCN and C2H2 into CNTs. The energies involved in these processes, as well as the changes in molecular structure and electronic properties of the dopants and the CNTs are discussed and rationalized by the amount of charge transferred between dopant and CNT.
Full geometric optimization of endo,endo-tetracyclo[4.2.1.13,6.02,7]dodeca-4,9-diene (TTDD) has been carried out by ab initio and DFT/B3LYP methods and the structure of the molecule investigated. The double bonds of TTDD molecule are endo pyramidalized. The structure of π-orbitals and their mutual interactions for TTDD molecule were investigated. The cationic
intermediates and products obtained as a result of the addition reaction have been studied using the HF/6-311G(d), HF/6-311G(d,p)
and B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable N- and U-type cations and the difference
between the stability of these cations is small. The N- and U-type reaction products are obtained as a result of the reaction,
which takes place via the cations in question. The stability of exo, exo and exo, endo isomers of N-type product are nearly the same and the formation of both isomers is feasible. The U-type product basically
formed from the exo, exo-isomer. Although the U-type cation was 0.68 kcal mol−1 more stable than the N-type cation, the U-type product was 4.79 kcal mol−1 less stable than the N-type product.
Figure The energy diagram of TTDD–Br2 system (kcal mol−1)(MP2/6-311G*//HF/6-311G*) 相似文献
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
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
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
The C2 fragmentation energies of the most stable isolated-pentagon-rule (IPR) isomers of the C80 and C82 fullerenes were evaluated with second-order Møller-Plesset (MP2) theory, density-functional theory (DFT) and the semiempirical self-consistent charge density-functional tight-binding (SCC-DFTB) method. Zero-point energy, ionization energy and empirical C2 corrections were included in the calculation of fragmentation energies for comparison with experimental C2 fragmentation energies of the fullerene cations. In the case of the most probable Stone-Wales pathway of C2 fragmentation of C80, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{80}}}} ^{ + } } \right)}\) agree well with experimental data, whereas in the case of C82 fragmentation, the calculated \(D_{0} {\left( {{\text{C}}_{{{\text{82}}}} ^{ + } } \right)}\) exceed by up to 1.2 eV the experimental ones, which suggests that other IPR isomers may be present in sufficient amounts in experimental samples. Computer-intensive MP2 calculations and DFT calculations with larger basis sets do not yield much improved C2 fragmentation energies, compared to those reported earlier with B3LYP/3-21G. On the other hand, semiempirical approaches such as SCC-DFTB, which are orders of magnitude less intensive, yield satisfactory fragmentation energies for higher fullerenes and may become a method of choice for routine calculations of fullerenes and carbon nanotubes.
Figure C2 fragmentation energies of C80 and C82 fullerenes have been calculated with B3LYP/6-31G* model chemistry, with semiempirical self-consistent-charge density-functional tight-binding (SCC-DFTB) method and with the more rigorous MP2 method. The influence of basis set extension and level of theory on the resulting fragmentation energies is discussed
