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Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, have been performed to investigate the local hydration structure and dynamics of carbonate (CO(3)(2-)) in dilute aqueous solution. With respect to the QM/MM scheme, the QM region, which contains the CO(3)(2-) and its surrounding water molecules, was treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set, while the rest of the system is described by classical MM potentials. For both the HF/MM and B3LYP/MM simulations, it is observed that the hydrogen bonds between CO(3)(2-) oxygens and their nearest-neighbor waters are relatively strong, i.e., compared to water-water hydrogen bonds in the bulk, and that the first shell of each CO(3)(2-) oxygen atom somewhat overlaps with the others, which allows migration of water molecules among the coordinating sites to exist. In addition, it is observed that first-shell waters are either "loosely" or "tightly" bound to the respective CO(3)(2-) oxygen atoms, leading to large fluctuations in the number of first-shell waters, ranging from 1 to 6 (HF/MM) and 2 to 7 (B3LYP/MM), with the prevalent value of 3. Upon comparing the HF and B3LYP methods in describing this hydrated ion, the latter is found to overestimate the hydrogen-bond strength in the CO(3)(2-)-water complexes, resulting in a slightly more compact hydration structure at each of the CO(3)(2-) oxygens.  相似文献   

3.
In the context of our detailed study of the chemical behavior of aquo- and ammine-Zn(II) complexes, ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations were performed at the Hartree-Fock (HF) level for the zinc(II)-diamine complexes in aqueous solution. The initial structures of cis and trans isomers of the tetraaquodiamminezinc(II) complex were found to transform into the triaquodiamminezinc(II) complex by releasing one water ligand after approximately 6 and approximately 22 ps of simulation time, respectively. The structural and dynamical properties of these three zinc complexes, i.e., cis-[Zn(NH3)2(H2O)4]2+, trans-[Zn(NH3)2(H2O)4]2+, and [Zn(NH3)2(H2O)3]2+, were analyzed in terms of radial distribution functions (RDF), coordination number distributions (CND), angular distribution functions (ADF), tilt and theta angle distributions, ligands' mean residence times (MRTs), and ion-ligand stretching frequencies. One considerably elongated Zn-O bond of 2.43 A was observed in the case of the cis isomer for one of the water ligands located in the trans position to an ammonia ligand. In the trans isomer the average Zn-O bond length was observed to be 2.23 A, while in the triaquodiamminezinc(II) complex two distinct Zn-O bonds, namely 2.12 A for the ligands in the trigonal plane and 2.26 A for axial water molecules, were observed. As both of the octahedral isomers are transformed into the pentacoordinated structure within the picosecond range, they might be regarded as "metastable species or intermediates", while the triaquodiamminezinc(II) complex is the most stable species of the zinc(II)-diamine complex in aqueous solution.  相似文献   

4.
Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.  相似文献   

5.
BP86, B3LYP and MP2 methods, generally used to study large systems containing transition metals, were compared for their ability to accuratly evaluate bond dissociation energies of copper complexes. Various [Cu-L]+ and [Cu-L]2+ complexes in which L are small ligands and the higher coordinated complexes, [Cu(NH3)(4)]+ and [Cu(NH3)4]2+ were studied. For monoligated complexes, the BDEs calculated by the three methods differed by 2 to 60 kcal/mol, the larger differences being obtained for [Cu-L]2+ complexes. The BDEs calculated using the B3LYP functional were in general close to the experimental values whereas the BDEs calculated using the BP86 functional were too high and the BDEs calculated using the MP2 were too low. If we rank the whole ligands according to their increased bond strength, the resulting orders obtained with the three methods are different for the [Cu-L]+ complexes, the B3LYP giving the same order as the experimental one. This result indicates that the BDEs of [Cu-L]+ complexes are better modeled using the B3LYP than using the BP86 and MP2 methods. For [Cu-L]2+, B3LYP also gave the most reliable results whereas BP86 gave too large BDEs and MP2 gave too small BDEs. However, symmetries of ground states can be different using DFT and post-Hartree-Fock methods. For [Cu-N2O]2+ the use of the B1LYP provides a better symmetry of the complex than the B3LYP, as has been recently shown in the literature for [Cu-H2O]2+. MP2 led to an incorrect bent structure for [Cu-N2]2+ in contrast to a linear structure obtained with the other methods, including CCSD(T). However, due to the lack of experimental data for [Cu-L]2+ complexes and to contrasted results for the methods, it is not possible to conclude definitely. For the high coordinated complexes [Cu(NH3)4]+ and [Cu(NH3)4]2+, the PBE calculation method was used in addition to the BP86, B3LYP and MP2. The BDE values were very close to each other when there is no change of the oxidation state during the reaction. On the basis of these calculations, the choice of the method was less crucial for high coordinated complexes [Cu(NH3)4]+ and [Cu(NH3)4]2+ so long as the oxidation state remained the same during the reaction. In contrast, when [Cu(NH3)4]2+ is reduced in [Cu(NH3)3]+ and NH3, the BDE calculated using the four methods were markedly different.  相似文献   

6.
A novel (N6O4) macrocyclic ligand (L) and its Cu(II) complexes have been prepared and characterized by elemental analysis, spectral, thermal (TG/DTG), magnetic, and conductivity measurements. Quantum chemical calculations have also been carried out at B3LYP/6-31+G(d,p) to study the structure of the ligand and one of its complexes. The results show a novel macrocyclic ligand with potential amide oxygen atom, amide and amine nitrogen atoms available for coordination. Distorted square pyramidal ([Cu(L)Cl]Cl·2.5H2O (1), [Cu(L)NO3]NO(3)·3.5H2O (2), and [Cu(L)Br]Br·3H2O (4) and octahedral ([Cu(L)(OAc)2]·5H2O (3)) geometries were proposed. The EPR data of 1, 2, and 4 indicate d1x2(-y)2 ground state of Cu(II) ion with a considerable exchange interaction. The measured cytotoxicity for L and its complexes (1, 2) against three tumor cell lines showed that coordination improves the antitumor activity of the ligand; IC50 for breast cancer cells are ≈8.5, 3, and 4 μg/mL for L and complexes (1) and (2), respectively.  相似文献   

7.

The most practicable complexes formed between Cryptand[2.2.2] and hydrated Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) cations (denoted as [ML]+2) were modeled using computational chemistry methods. The energies of complexation reactions were calculated in both gas phase and solution at B3LYP/6-31+G(d) and B3LYP/6-311++G(3df,2pd) levels of theory. The accuracy of selected computational methods was confirmed with comparison between available X-ray data and computational results. The results suggested that [CuL]+2 and [CoL]+2 structures could be the most and the least stable systems, respectively. The nature of metal-ligand interactions based on quantum theory of atoms in molecule (QTAIM) was discussed for all the complexes. This analysis confirmed the ionic nature of metal-ligand interactions due to electron density values for M-O bonds and M-N interactions. Natural bond orbital (NBO) and natural energy decomposition analysis (NEDA) were utilized to explain more details of interaction between divalent cations and donor atoms of the ligand.

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8.
A novel polymeric one-dimensional compound Cu(tn)Cl2 (tn = 1,3-diaminopropane) was prepared and structurally characterized, and its spectral, magnetic, thermodynamic, and thermal properties were studied. The unique structure shows ladderlike chains composed of Cu(II) atoms and chloro bridging ligands [Cu(-mu(3)-Cl-)Cu2] running along the crystallographic c axis. The coordination geometry about copper (4 + 2) approximates that of a strongly elongated octahedron. The equatorial plane of the coordination octahedron is formed by a chelate N-bonded tn ligand and two chloro ligands. One of the chloro ligands is terminal, and the other one, mu3-Cl-, forms two additional longer bonds to the neighboring copper atoms and thus occupies the axial octahedral positions. The electronic ground state of the Cu(II) ion is of d(z)2 symmetry and suggests the activation of intraladder and interladder Cl...H-N hydrogen bonds as exchange paths that form a two-dimensional pattern of a triangular symmetry. The interaction due to the hydrogen bonds seems to play an important role in molecular packing and magnetic coupling. The studies of magneto-structural correlations including electron paramagnetic resonance measurements and thermodynamic and magnetic properties revealed a two-dimensional character of magnetic correlations with the effective intralayer exchange coupling J/k(B) approximately -3 K. No phase transition to the ordered state has been observed down to 60 mK. Cu(tn)Cl2 with the interlayer coupling J' approximately 10(-3)J and moderate intralayer interaction represents an excellent example of a two-dimensional magnetic system.  相似文献   

9.
The structure optimizations of picolinaldehyde N-oxide thiosemicarbazone (Hpiotsc), 2-benzoylpyridine semicarbazone (H2BzPS), their imino tautomers and their complexes with Ni(II), Cu(II), and Zn(II) were carried out using DFT calculations. The structures of Hpiotsc and H2BzPS ligands, transition states of their tautomerizations were obtained at the B3LYP/6-31+G(d,p) level and their thermodynamic properties were derived from the frequency calculations at the same level of theory. The B3LYP/LANL2DZ-optimized structures of Hpiotsc and H2BzPS complexes with Ni(II), Cu(II), and Zn(II), and the thermodynamic properties of their complexations derived from the B3LYP/LANL2DZ-frequency calculations were obtained. The B3LYP/LANL2DZ-optimized geometrical parameters for the [Ni(Hpiotsc)2]2+, [Cu(Hpiotsc).Cl2], and [Zn(Hpiotsc).Cl2] complexes show good agreement with their corresponding X-ray crystallographic data.  相似文献   

10.
A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.  相似文献   

11.
The azo dye ligand N-diaminomethylene-4-(3-formyl-4-hydroxy-phenylazo)-benzenesulfonamide (HL) and Cu(II), Co(II), and Mn(II) coordination polymers were synthesized in addition to a non-polymeric Pd(II) complex. In all complexes, the ligand bonds to the metal ion through the formyl and α-hydroxy oxygen atoms. The sulfonamide oxygen also coordinates to the metal. The complexes are formulated as [ML2] n , where M?=?Cu(II), Co(II), and Mn(II), and [ML(Cl)(H2O)], where M?=?Pd(II). On the basis of spectral studies and magnetic susceptibility measurements, an octahedral geometry was assigned to Co(II) and Mn(II) complexes, tetragonally elongated octahedral geometry for Cu(II) complex, while the Pd(II) complex was found to be square planar. Crystallization of Cu(II) complex from DMF afforded single crystals of general formula {[Cu(L)2]?·?3DMF} n (2). X-ray structural analysis of 2 revealed that each Cu(II) adopts elongated octahedral geometry affording 1-D chains. The chains are connected by hydrogen bonds, resulting in the formation of 2-D supramolecular assemblies. The crystal structure of HL has also been determined and discussed. Cyclic voltammetric behavior of the ligand and some complexes are also discussed.  相似文献   

12.
The nature of the bonding in model complexes of di-copper metalloenzymes has been analyzed by means of the electronic localization function (ELF) and by the quantum theory of atoms in molecules (QTAIM). The constrained space orbital variations (CSOV) approach has also been used. Density functional theory (DFT) and CASSCF calculations have been carried out on several models of tyrosinase such as the sole Cu2O22+ central core, the Cu2O2(NH3)62+ complex and the Cu2O2(Imidazol)62+ complex. The influence on the central Cu(2)O(2) moiety of both levels of calculation and ligand environment have been discussed. The distinct bonding modes have been characterized for the two major known structures: [Cu(2)(mu-eta(2): eta(2)-O(2))](2+) and [Cu(2)(mu-O(2))](2+). Particular attention has been given to the analysis of the O-O and Cu-O bonds and the nature of the bonding modes has also been analyzed in terms of mesomeric structures. The ELF topological approach shows a significant conservation of the topology between the DFT and CASSCF approaches. Particularly, three-center Cu-O-Cu bonds are observed when the ligands are attached to the central core. At the DFT level, the importance of self interaction effects are emphasized. Although, the DFT approach does not appear to be suitable for the computation of the electronic structure of the isolated Cu(2)O(2) central core, competitive self interaction mechanisms lead to an imperfect but acceptable model when using imidazol ligands. Our results confirm to a certain extent the observations of [M.F. Rode, H.J. Werner, Theoretical Chemistry Accounts 4-5 (2005) 247.] who found a qualitative agreement between B3LYP and localized MRCI calculations when dealing with the Cu(2)O(2) central core with six ammonia ligands.  相似文献   

13.
The structural and dynamical properties of NO3- in dilute aqueous solution have been investigated by means of two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely HF/MM and B3LYP/MM, in which the ion and its surrounding water molecules were treated at HF and B3LYP levels of accuracy, respectively, using the DZV+ basis set. On the basis of both HF and B3LYP methods, a well-defined first hydration shell of NO3- is obtainable, but the shell is quite flexible and the hydrogen-bond interactions between NO3- and water are rather weak. With respect to the detailed analysis of the geometrical arrangement and vibrations of NO3-, the experimentally observed solvent-induced symmetry breaking of the ion is well reflected. In addition, the dynamical information, i.e., the bond distortions and shifts in the corresponding bending and stretching frequencies as well as the mean residence time of water molecules surrounding the NO3- ion, clearly indicates the "structure-breaking" ability of this ion in aqueous solution. From a methodical point of view it seems that both the HF and B3LYP methods are not too different in describing this hydrated ion by means of a QM/MM simulation. However, the detailed analysis of the dynamics properties indicates a better suitability of the HF method compared to the B3LYP-DFT approach.  相似文献   

14.
Systematic evaluation of method and basis set on the structure and energetics of organocuprate(I) and organocopper(III) species has been carried out. Various structures of organocuprate(I) and organocuprate(III) complexes were optimized with the HF, MP2, and B3LYP methods, and compared with the structures determined by X-ray crystallography (i.e., Me(2)Cu(I)(-), (CF(3))(4)Cu(III)(-)). Both the MP2 and B3LYP methods reasonably reproduce the X-ray structures while the HF method does not. Using larger basis set and incorporating the relativistic effects for Cu afford the best results. In the studies on the energetics of a Libond;Cu cluster model (Me(2)CuLi. LiCl) and Me(3)Cu model with the MP2, MP3, MP4DQ, MP4SDQ, CCSD(T), and B3LYP methods, the B3LYP method gives energetics similar to those obtained with the CCSD(T) method with much less cost, and hence, is judged to be the best practical method. The studies have shown that B3LYP method with the basis set incorporating the relativistic effective core potentials for Cu and the 6-31G* basis set for the rest is the theoretical method that is the most cost-effective for the studies of the structure and energetics of organocuprate(I) and organocopper(III) species.  相似文献   

15.
Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, namely B3LYP/MM and MP2/MM, have been performed to investigate the possible influence of electron correlation on the structure and dynamics of the H(3)O(+) hydrate. In comparison to the previously published HF/MM results, both B3LYP/MM and MP2/MM simulations clearly reveal stronger H(3)O(+)-water hydrogen bond interactions, which are reflected in a slightly greater compactness of the H(3)O(+) hydrate. However, the B3LYP/MM simulation, although providing structural details very close to the MP2/MM data, shows an artificially slow dynamic nature of some first shell water molecules as a consequence of the formation of a long-lived H(3)O(+)···H(2)O hydrogen bonding structure.  相似文献   

16.
The structure of reversibly oxidizable [Cu(mmb)2](BF4) with 1-methyl-2-(methylthiomethyl)-1H-benzimidazole (mmb) as bidentate N,S-donor ligand has been determined and compared with that of the copper(II) species [Cu(mmb)2(eta 1-ClO4)](ClO4). In the complex ions of the equilibrium [CuI(mmb)2](+) + ClO4- reversible e- + [CuII(mmb)2-(eta 1-ClO4)]+ the almost linear N-Cu-N backbone is invariant whereas the bonds to the thioether sulfur centers and especially the changing S-Cu-S angle (145.18(5) degrees for the CuII species, 109.33(3) degrees for the CuI form) reflect the metal oxidation state. In contrast to the perchlorate coordinating copper(II) species, [CuI(mmb)2](BF4) contains a cation with a very large vacant site at the metal center, resulting in elliptical channels within the crystal. DFT calculations on [CuI(mb)2]+, [CuII(mb)2]2+, and [CuII(mb)2(OClO3)]+ with mb = 2-methylthiomethyl-1H-benzimidazole confirm the essential role of the metal-sulfur bonds in responding to the reversible CuI/II electron transfer process, even in the absence of electronically stronger interacting thiolate sulfur centers or sophisticated oligodentate ligands.  相似文献   

17.
A direct dynamics simulation at the B3LYP/6-311+G(d,p) level of theory was used to study the F- + CH3OOH reaction dynamics. The simulations are in excellent agreement with a previous experimental study (J. Am. Chem. Soc. 2002, 124, 3196). Two product channels, HF + CH2O + OH- and HF + CH3OO-, are observed. The former dominates and occurs via an ECO2 mechanism in which F- attacks the CH3- group, abstracting a proton. Concertedly, a carbon-oxygen double bond is formed and OH- is eliminated. Somewhat surprisingly this is not the reaction path, predicted by the intrinsic reaction coordinate (IRC), which leads to a deep potential energy minimum for the CH2(OH)2...F- complex followed by dissociation to HF + CH2(OH)O-. None of the direct dynamics trajectories followed this path, which has an energy release of -63 kcal/mol and is considerably more exothermic than the ECO2 path whose energy release is -27 kcal/mol. Other product channels not observed, and which have a lower energy than that for the ECO2 path, are F- + CO + H2 + H2O (-43 kcal/mol), F- + CH2O + H2O (-51 kcal/mol), and F- + CH2(OH)2 (-60 kcal/mol). Formation of the CH3OOH...F- complex, with randomization of its internal energy, is important, and this complex dissociates via the ECO2 mechanism. Trajectories which form HF + CH3OO- are nonstatistical events and, for the 4 ps direct dynamics simulation, are not mediated by the CH3OOH...F- complex. Dissociation of this complex to form HF + CH3OO- may occur on longer time scales.  相似文献   

18.
[Cu(4)L(2)(bpy)(4)(H(2)O)(3)](ClO(4))(4).2.5H(2)O, 1, a new tetranuclear Cu(II) cluster showing square planar geometry, formed with aspartate bridging ligand (L) has been synthesized. The global magnetic coupling is ferromagnetic but theoretical DFT/B3LYP calculations are necessary to assign which Cu-L-Cu side is ferro or antiferromagnetically coupled.  相似文献   

19.
The Fe4S4 complex {(CH3)3NCH2CONH2}2[Fe4S4((tBuS)4] (1) was synthesized to replicate the ferredoxin active site with a subset of its N-H...S hydrogen bonds. The two cationic counterions mimic the polypeptide backbone of ferredoxin (Fd) as amide hydrogen-bond donors to sulfur atoms of the iron-sulfur cluster. X-ray crystallographic data show that the organic sulfur (Sgamma) of one tert-butylthiolate ligand and one inorganic sulfur of the cluster core serve as N-H...S hydrogen-bond acceptors. The cluster core of complex 1 is tetragonally elongated in contrast to that of Fd, which is tetragonally compressed. This is the first observation of an elongated [Fe4S4]2+ cluster core. Additionally, this is the first synthetic Fd model in which N-H...S hydrogen bonding to a cluster has been achieved.  相似文献   

20.
B3LYP* functionals were used to model the sixteen iron(II) (1A, LS and 5T, HS) and iron(III) (2T, LS and 6A, HS) complexes of the 1:3 Schiff base condensate of tris(2-aminoethyl)amine and imidazole-4-carboxaldehyde, H3L1, and its deprotonated forms, [H2L1]1-, [HL1]2-, and [L1]3-. This ligand system is unusual in that [FeH3L1]3+, [FeH3L1]2+ and [FeL1]- all exhibit a spin crossover between 100-300 K. This makes these complexes ideal for a hybrid DFT computational approach and provides an opportunity to refine the value of the exact exchange admixture parameter, c3, and to predict properties of partially protonated complexes that are not experimentally available. The accepted value of 0.20 is larger than the value of approximately 0.13 that was found to best reproduce experimental data in terms of spin state predictions. With iron(III) B3LYP calculations showed that all of the complexes were low spin at 298 K with the exception of [FeH3L1]3+ which is spin crossover in agreement with experimental results. It was also shown for iron(III) that the ligand field increased as the number of protons decreased. In contrast all of the iron(II) complexes were close to the spin crossover region regardless of protonation state. Experimental structures are fairly well modeled by this system in regard to the key structural indicators of spin state, which are the bite and trans angles. The calculated iron to nitrogen atom distances are always larger in the high spin form than the low spin form but all iron to nitrogen bond distances are larger than the experimental values. In general non-bonded interactions are not well modeled by this methodology.  相似文献   

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