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1.
Within the quantum theory of atoms in molecules (QTAIM) framework we present a quantum topology phase diagram (QTPD) using the Poincaré–Hopf relation of a total of 17 all new QTAIM topologies of the cis‐ and trans‐isomers of the cyclic contryphan‐Sm peptide. The resultant QTPD consists of separate regions for the cis‐ and trans‐isomers that only overlap for topologies associated with the lowest energy minima of the cis‐ and trans‐isomers. We determine the QTAIM topologies of 29 “missing” isomers. A new, contracted formulation of the QTPD is presented, this contracted formulation includes the interamino acid bond critical points (BCPs) that link together the amino acid units, the disulphide bridge “pivot” BCP and side chain bonding interactions. The seven interamino acid BCPs linking the amino acid units coincide with the so‐called peptide backbone, the conventional qualitative approach to reduce the complexity of the peptide. We expand the interpretation of ellipticity to include the associated eigenvectors and find that higher values of the ellipticity ? are associated with a greater preference to conserve folding states. We quantify previous qualitative findings that suggested the disulfide bond is central to the folding behavior of the cyclic contryphan‐Sm peptide and why the cis‐isomer is the major form of the cyclic contryphan‐Sm peptide. © 2014 Wiley Periodicals, Inc.  相似文献   

2.
Using the quantum theory of atoms in molecules a near complete combined directed spanning quantum topology phase diagram (QTPD) was constructed from the nine (H2O)5 reaction‐pathways and five unique Poincaré–Hopf solutions that were found after an extensive search of the MP2 potential energy surface. Two new energy minima that were predicted from earlier work are found and include the first (H2O)5 conformer with a 3‐DQT quantum topology. The stress tensor Poincaré–Hopf relation indicated a preference for 2‐DQT (H2O)5 topologies as well as the presence of coupling between shared‐shell O? H BCPs to the hydrogen‐bond BCPs that share an H NCP. The complexity of the near complete combined QTPD was explained in terms of the O…O bonding interactions that were found in six of the nine (H2O)5 reaction‐pathways and for all points of the combined QTPD. The stabilizing role of the O…O bonding interactions from the values of the total local energy density was explored. © 2016 Wiley Periodicals, Inc.  相似文献   

3.
A straightforward discussion on how to generate molecular fields is developed within the postulates of quantum mechanics. The theoretical formalism points towards the generalization and extension of the well-known molecular field forms, associated to density function and electrostatic molecular potential (EMP), including another category of fields associated to quantum molecular similarity measures. The results show that the new formalism can be easily applied to obtain an unlimited number of new information about molecular behavior.  相似文献   

4.
The enhancing effects of molecule X (X = PH2Cl, SHCl, ClCl) on S···S and Se···Se chalcogen–chalcogen bonds in the cyclic trimers SHCl···SHCl···X and SeHCl···SeHCl···X were investigated by calculations at the MP2/aug‐cc‐pVTZ level. When molecule X is added to the dimer SHCl···SHCl (SeHCl···SeHCl), cyclic trimers are formed. Compared with the dimer, all the cyclic trimers have shorter S···S (Se···Se) lengths, greater electron densities, negative three‐body interaction energies, and larger second‐order perturbation energies. These results indicate that the addition of molecule X strengthens the original S···S (Se···Se) bond. For the SHCl···SHCl···X cyclic trimers, the S···S bond is strongest in SHCl···SHCl···PH2Cl, weaker in SHCl···SHCl···SHCl, and weakest in SHCl···SHCl···ClCl. This same trend is observed for the Se···Se bond in SeHCl···SeHCl···X. This means that PH2Cl provides the greatest enhancement to the S···S (Se···Se) interaction.  相似文献   

5.
Electronic structures and properties of several anions, metal cations, and their complexes with neutral molecules were investigated at the HF/6‐31G** and B3LYP/6‐31G** levels of theory. Charges shifted from atomic sites due to atomic orbital hybridization called hybridization displacement charges (HDC) were investigated in detail. It has been found that many components of HDC are associated with each atom of ion that are shifted from the atomic sites, those associated with metal cations being shifted by large distances as found previously in electrically neutral systems. It is shown that atomic orbitals are appreciably rehybridized in going from neutral molecules to anions and cations. Molecular dipole moments and surface molecular electrostatic potentials (MEP) are obtained satisfactorily using HDC for the various types of species mentioned above. In the OH?? H2O complex, reversal of direction of shift of an HDC component associated with the hydrogen atom of H2O involved in hydrogen bonding, indicates that the hydrogen bond between OH? and H2O would have some covalent character. Other atomic site‐based point charge models cannot provide such information about the nature of bonding. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem 2007  相似文献   

6.
Interaction with the ligand binding domain of receptors for natural chemicals present one potential mechanism for the biological effects of environmental chemicals. Evidence suggests that the electrostatic interaction between the ligand and the receptor is an important component for binding to some of the relevant receptors. The presence of charged residues near the binding site suggests that the charge distribution of the free ligand may be different from the charge distribution of the ligand as it approaches the binding domain of the protein. In this study a new type of potential is computed for a series of dibenzo-p-dioxin (dioxin) ligands. This quantum mechanically computed potential results from interaction between the ligand and a trimethyl ammonium probe at a set of grid points. This interaction potential is compared with the molecular electrostatic potential computed from the wave function of the isolated ligands. Three types of local minima are found: (1) above the oxygen; (2) above the conjugated ring; and (3) above the chlorine(s). The molecular electrostatic potential emphasizes the minima associated with the chlorine atoms and, in that potential, the minima associated with the oxygen atoms disappear with chlorination. In the new potential, the minima over the oxygen atoms are maintained even in tetrachlorodioxin. As chlorination is increased the differences between the two potentials increases. The new potential shows the influence of the π-cation interaction, which is largest when there is little substitution on the ring. The presence of the probe induces a dipole component of 1 debye perpendicular to the plane of the ligand. Local minima in the interaction potential are then used as starting structures for the determination of the most stable ligand–probe complexes. The most stable structures are obtained from the minima associated with the oxygen atoms. These structures are stabilized by a hydrogen bond formation between the probe and the oxygen and the molecule is bent by 30° about the O(SINGLE BOND)O axis. For this series of molecules, the new potential retains some of the features that determine the hydrogen bond whereas the molecular electrostatic potential does not. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 673–684, 1998  相似文献   

7.
Different density functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, experiment. The agreement between the CCSD(T) results and experiment, when available, is good. The agreement is also good between bond strengths calculated at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calculations systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calculations are generally in good agreement with the CCSD(T) results.Contribution to the Björn Roos Honorary Issue  相似文献   

8.
Simulated tempering (ST) is a generalized‐ensemble algorithm that employs trajectories exploring a range of temperatures to effectively sample rugged energy landscapes. When implemented using the molecular dynamics method, ST can require the use of short time steps for ensuring the stability of trajectories at high temperatures. To address this shortcoming, a mass‐scaling ST (MSST) method is presented in which the particle mass is scaled in proportion to the temperature. Mass scaling in the MSST method leads to velocity distributions that are independent of temperature and eliminates the need for velocity scaling after the accepted temperature updates that are required in conventional ST simulations. The homogeneity in time scales with changing temperature improves the stability of simulations and allows for the use of longer time steps at high temperatures. As a result, the MSST is found to be more efficient than the standard ST method, particularly for cases in which a large temperature range is employed. © 2016 Wiley Periodicals, Inc.  相似文献   

9.
10.
CF3H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug‐cc‐pVDZ calculations. The binding energy of monoanions halide, NO3?, formate, acetate, HSO4?, and H2PO4? lie in the 12–17 kcal mol?1 range, although F? is more strongly bound, by 26 kcal mol?1. Dianions SO42? and HPO42? are bound by 27 kcal mol?1, and trianion PO43? by 45 kcal mol?1. When two O atoms are available on the anion, the CH???O? H‐bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.  相似文献   

11.
Ab initio calculations have been performed on a series of complexes formed between halogen-containing molecules and ammonia to gain a deeper insight into the nature of halogen bonding. It appears that the dihalogen molecules form the strongest halogen-bonded complexes with ammonia, followed by HOX; the charge-transfer-type contribution has been demonstrated to dominate the halogen bonding in these complexes. For the complexes involving carbon-bound halogen molecules, our calculations clearly indicate that electrostatic interactions are mainly responsible for their binding energies. Whereas the halogen-bond strength is significantly enhanced by progressive fluorine substitution, the substitution of a hydrogen atom by a methyl group in the CH(3)X...NH(3) complex weakened the halogen bonding. Moreover, remote substituent effects have also been noted in the complexes of halobenzenes with different para substituents. The influence of the hybridization state of the carbon atom bonded to the halogen atom has also been examined and the results reveal that halogen-bond strengths decrease in the order HC triple bond CX > H(2)C=CHX approximately O=CHX approximately C(6)H(5)X > CH(3)X. In addition, several excellent linear correlations have been established between the interaction energies and both the amount of charge transfer and the electrostatic potentials corresponding to an electron density of 0.002 au along the R-X axis; these correlations provide good models with which to evaluate the electron-accepting abilities of the covalently bonded halogen atoms. Finally, some positively charged halogen-bonded systems have been investigated and the effect of the charge has been discussed.  相似文献   

12.
We present a systematic study on the reliability of different theoretical methods to represent the molecular electrostatic potential (MEP), and MEP-derived properties of prototypical compounds containing phosphorus, sulfur and chlorine. Calculations at the Hartree-Fock and M?ller-Plesset up to fourth-order level of theory, as well as local, non-local and hybrid density functional computations were performed for a representative set of neutral molecules. The study was carried out using different basis sets ranging from the medium-sized 6-31G(d ) to the large 6-31G(2d,2p) basis set, but in some test calculations more extended basis sets were also considered. The analysis of the results was performed discussing separately the effect of the basis set and of the level of theory used to determine the molecular wavefunction on the reliability of the MEP and MEP-derived properties. Received: 4 March 1997 / Accepted: 27 June 1997  相似文献   

13.
A new intermolecular force field for nitrogen atoms in organic molecules was derived from a training dataset of 76 observed azahydrocarbon crystal structures and 11 observed heats of sublimation. The previously published W99 force field for hydrogen, carbon, and oxygen was thus extended to include nitrogen atoms. Nitrogen atoms were divided into four classes: N(1) for triply bonded nitrogen, N(2) for nitrogen with no bonded hydrogen (except the triple bonded case), N(3) for nitrogen with one bonded hydrogen, and N(4) for nitrogen with two or more bonded hydrogens. H(4) designated hydrogen bonded to nitrogen. Wavefunctions of 6‐31g** quality were calculated for each molecule and the molecular electric potential (MEP) was modeled with net atomic and supplementary site charges. Lone pair electron charge sites were included for nitrogen atoms where appropriate, and methylene bisector charges were used for CH2 and CH3 groups when fitting the MEP. X? H bond distances were set to standard values for the wave function calculation and then foreshortened by 0.1 Å for the MEP and force field fitting. Using the force field optimized to the training dataset, each azahydrocarbon crystal structure was relaxed by intermolecular energy minimization. Predicted maximum changes in unit cell edge lengths for each crystal were 3% or less. The complete force field for H, C, N, and O atoms was tested by intermolecular energy relaxation of nucleoside and peptide molecular crystals. Even though these molecules were not included in any of the training datasets for the force field, agreement with their observed crystal structures was very good, with predicted unit cell edge shifts usually less than 2%. These tests included crystal structures of representatives of all eight common nucleosides found in DNA and RNA, 15 dipeptides, four tripeptides, two tetrapeptides, and a pentapeptide with two molecules in the asymmetric unit. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1154–1166, 2001  相似文献   

14.
Electronic structure and spectroscopic properties for the ground electronic states of CH, SiH, GeH and SnH molecules were obtained using the multiconfigurational self-consistent field followed by spin–orbit multireference multistate perturbation theory. Spin–orbit splitting calculations for ground states of the four molecules were carried out with model core potential (MCP) and all-electron (AE) methods. MCP results are compared with corresponding AE values to estimate the accuracy of the saving cost MCP calculations. The potential energy curves, calculated for the Ω states CH(X12Π1/2 and X22Π3/2), SiH(X12Π1/2 and X22Π3/2), GeH(X12Π1/2 and X22Π3/2) and SnH(X12Π1/2 and X22Π3/2) using the MCP method, were fitted to analytical potential energy function using Murrell–Sorbie potential energy function. Based on the analytical potential energy function, force constants and spectroscopic constants for the Ω states were obtained.  相似文献   

15.
The dimensional analyses of the position and momentum variances‐based quantum mechanical Heisenberg uncertainty measure, as well as the entropic information measures given by the Shannon information entropy sum and the product of Fisher information measures are carried out for two widely used nonrelativistic isotropic exponential‐cosine screened Coulomb potentials generated by multiplying the superpositions of (i) Yukawa‐like, ?Z(er/r), and (ii) Hulthén‐like, ?Zμ(1/(eμr ? 1)), potentials by cos(bμr) followed by addition of the term a/r2, where a and b ≥ 0, μ are the screening parameters and Z, in case of atoms, denotes the nuclear charge. Under the spherical symmetry, all the information measures considered are shown to be independent of the scaling of the set [μ, Z] at a fixed value of μ/Z, a, and b and the other parameters defining the superpositions of the potentials. Numerical results are presented, which support the validity of the scaling properties. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007  相似文献   

16.
The structures, stabilities, nature of bonding, and potential energy surfaces of low‐energy isomers of planar CnB5 (n = 1?7) have been systematically explored at the CCSD(T)/6‐311+G(d)//B3LYP/6‐311+G(d) level. Incremental binding energy (IBE) and second order energy difference (Δ2E) analyses demonstrate that CnB5 clusters with even n have relatively higher stability. The nature of bonding in these clusters is discussed based on valence molecular orbital (VMO), and Mayer bond order (MBO). Hückel (4n + 2) rule and nucleus‐independent chemical shift (NICS) values suggest that the ground states of C3B5, C4B5, and C7B5 have π aromaticity. VMO, electron localization function (ELF), adaptive natural density partitioning (AdNDP), and NICS analyses reveal the double aromaticity of C3B5 cation. CB5 and C3B5 are stable both thermodynamically and kinetically based on isomerization analysis. In addition, the simulated IR spectra are expected to be helpful for future experimental studies of these clusters.  相似文献   

17.
An efficient implementation of the canonical molecular dynamics simulation using the reversible reference system propagator algorithm (r‐RESPA) combined with the particle mesh Ewald method (PMEM) and with the macroscopic expansion of the fast multipole method (MEFMM) was examined. The performance of the calculations was evaluated for systems with 3000, 9999, 30,000, 60,000, and 99,840 particles. For a given accuracy, the optimal conditions for minimizing the CPU time for the implementation of the Ewald method, the PMEM, and the MEFMM were first analyzed. Using the optimal conditions, we evaluated the performance and the reliability of the integrated methods. For all the systems examined, the r‐RESPA with the PMEM was about twice as fast as the r‐RESPA with the MEFMM. The difference arose from the difference in the numerical complexities of the fast Fourier transform in the PMEM and from the transformation of the multipole moments into the coefficients of the local field expansion in the MEFMM. Compared with conventional methods, such as the velocity‐verlet algorithm with the Ewald method, significant speedups were obtained by the integrated methods; the speedup of the calculation was a function of system size, and was a factor of 100 for a system with 3000 particles and increased to a factor of 700 for a system with 99,840 particles. These integrated calculations are, therefore, promising for realizing large‐scale molecular dynamics simulations for complex systems. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 201–217, 2000  相似文献   

18.
Quantum information theory is applied to formulate a new technique for dealing with molecular similarity problems. In this technique, the so‐called quantum fidelity appears to be a counterpart of the conventional similarity measure due to Carbo (Carbo, R.; Leyda, L.; Arnau, M. Int J Quantum Chem 1980, 17, 1185). We define many‐body spin‐free density matrices for atoms and fragments in molecule, and compute corresponding fidelity measures for molecular subsystems. It allows us to treat the problem from the beginning within a many‐electron setting. The approach is employed for analyzing similarity between free atoms and atoms in molecule. A new chirality index, as based on the fidelity between molecule and its mirror image, is suggested to be an approximately additive nonnegative quantity. We also examine a local aromaticity by computing the fidelity measures for benzenoid fragments in polyaromatic hydrocarbons. A detailed study of the proposed indices is reported at the ab initio or semiempirical levels. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011  相似文献   

19.
Using ab initio calculations, we have investigated the possibility of formation of triangular XBr:SHX:PH2X complexes, where X = F, Cl, Br, CN, NC, OH, NH2, and OCH3. These complexes are formed through the interaction of a positive electrostatic potential region (σ‐hole) on a molecule with the negative region in another one. The results show that the combined halogen, chalcogen, and pnictogen interactions can give rise to stable cyclic structures. The interaction energies of these complexes span over a wide range, from ?3.55 to ?24.93 kcal/mol. Nice quadratic correlations are found between the interaction energies and binding distances in the trimers. To understand the nature of the interactions in these complexes, molecular electrostatic potential and quantum theory of atoms in molecule analyses are performed. © 2015 Wiley Periodicals, Inc.  相似文献   

20.
We describe in this work the copolymerization reaction of 3-trimethoxysilyl propyl methacrylate (MPS) with styrene (Styr.) and n-butyl acrylate (BuA) monomers through emulsion polymerization. The so-produced hybrid copolymer (P(BuA-co-MPS)) and terpolymer (P(Styr-co-BuA-co-MPS)) latexes were cast into films that displayed a good optical transparency. The copolymers microstructure in the films was characterized by FTIR, 13C and 29Si solid state NMR spectroscopies, and was found to be highly dependent on parameters such as the monomer feed composition, the suspension pH and the silane addition profile. The films obtained from the hybrid latexes showed improved dynamic mechanical properties indicating that a reinforcing organo-mineral network had formed in the composite materials. The dynamic modulus of the hybrids increased with increasing silane contents while, concurrently, the tan δ peak shifted to higher temperatures, broadened and decreased in intensity. To cite this article: S. Vitry et al., C. R. Chimie 6 (2003).  相似文献   

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