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1.
Halogen-bonding, a noncovalent interaction between a halogen atom X in one molecule and a negative site in another, plays critical roles in fields as diverse as molecular biology, drug design and material engineering. In this work, we have examined the strength and origin of halogen bonds between carbene CH2 and XCCY molecules, where X?=?Cl, Br, I, and Y?=?H, F, COF, COOH, CF3, NO2, CN, NH2, CH3, OH. These calculations have been carried out using M06-2X, MP2 and CCSD(T) methods, through analyses of surface electrostatic potentials V S(r) and intermolecular interaction energies. Not surprisingly, the strength of the halogen bonds in the CH2···XCCY complexes depend on the polarizability of the halogen X and the electron-withdrawing power of the Y group. It is revealed that for a given carbene···X interaction, the electrostatic term is slightly larger (i.e., more negative) than the dispersion term. Comparing the data for the chlorine, bromine and iodine substituted CH2···XCCY systems, it can be seen that both the polarization and dispersion components of the interaction energy increase with increasing halogen size. One can see that increasing the size and positive nature of a halogen’s σ-hole markedly enhances the electrostatic contribution of the halogen-bonding interaction. Graphical abstract
Halogen bonding interactions between carbene and X-CC-Y molecules (X?=?Cl, Br, and I; Y?=?H, F, COF, COOH, CF3, NO2, CN, OH, NH2, CH3) 相似文献
2.
Half sandwich complexes of the type [CpM(CO)nX] {X = Cl, Br, I; If, M = Fe, Ru; n = 2 and if M = Mo; n = 3} and [CpNiPPh3X] {X = Cl, Br, I} have been synthesized and their second order molecular nonlinearity (β) measured at 1064 nm in CHCl3 by the hyper-Rayleigh scattering technique. Iron complexes consistently display larger β values than ruthenium complexes while nickel complexes have marginally larger β values than iron complexes. In the presence of an acceptor ligand such as CO or PPh3, the role of the halogen atom is that of a π donor. The better overlap of Cl orbitals with Fe and Ni metal centres make Cl a better π donor than Br or I in the respective complexes. Consequently, M-π interaction is stronger in Fe/Ni-Cl complexes. The value of β decreases as one goes down the halogen group. For the complexes of 4d metal ions where the metal-ligand distance is larger, the influence of π orbital overlap appears to be less important, resulting in moderate changes in β as a function of halogen substitution. 相似文献
3.
A quantum chemistry study was carried out to investigate the strength and nature of halogen bond interactions in HXeH···XCCY complexes, where X = Cl, Br and Y = H, F, Cl, Br, CN, NC, C2H, CH3, OH, SH, NH2. Examination of the electrostatic potentials V(r) of the XCCY molecules reveals that the addition of substituents has a significant effect upon the most positive electrostatic potential on the surface of the interacting halogen atom. We found that the magnitude of atomic charges and multipole moments depends upon the halogen atom X and is rather sensitive to the electron-withdrawing/donating power of the remainder of the molecule. An excellent correlation was found between the most positive electrostatic potentials on the halogen atom and the interaction energies. For either HXeH···ClCCY or HXeH···BrCCY complexes, an approximate linear correlation between the interaction energies and halogens multipole moments are established, indicating that the electrostatic and polarization interactions are responsible for the stability of the complexes. According to energy decomposition analysis, it is revealed that the electrostatic interactions are the major source of the attraction in the HXeH···XCCY complexes. Furthermore, the changes in the electrostatic term are mainly responsible for the dependence of interaction energy on the halogen atom. Graphical abstract
Electrostatic potential mapped on the surface of molecular electron density at the 0.001 electrons Bohr ?3 of HXeH. The color ranges in kcal mol?1 red >8.5, yellow 1.5 to 8.5, green ?5.5 to 1.5, blue <?5.5. Black and blue circles are referred to surface maxima and minima, respectively. 相似文献
4.
《Bioorganic & medicinal chemistry》2016,24(20):4812-4825
A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the ‘sigma hole.’ Empirical force fields in which the electrostatic interactions are represented by atom-centered point charges cannot capture this effect because halogen atoms usually carry a negative charge and therefore interact unfavorably with other electronegative atoms. A strategy to overcome this problem is to attach a positively charged virtual particle to the halogen. In this work, we extend the additive CHARMM General Force Field (CGenFF) to include such interactions in model systems of phenyl-X, with X being Cl, Br or I including di- and trihalogenated species. The charges, Lennard-Jones parameters, and halogen-virtual particle distances were optimized to reproduce the orientation dependence of quantum mechanical interaction energies with water, acetone, and N-methylacetamide as well as experimental pure liquid properties and relative hydration free energies with respect to benzene. The resulting parameters were validated in molecular dynamics simulations on small-molecule crystals and on solvated protein–ligand complexes containing halogenated compounds. The inclusion of positive virtual sites leads to better agreement across experimental observables, including preservation of ligand binding poses as a direct result of the improved representation of halogen bonding. 相似文献
5.
6.
Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)
Mehdi D. Esrafili Fariba Mohammdain-Sabet Parvin Esmailpour 《Journal of molecular modeling》2013,19(11):4797-4804
Quantum chemical calculations are performed to study the interplay between halogen?nitrogen and halogen?carbene interactions in NCX?NCX?CH2 complexes, where X?=?F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that the X?N and X?Ccarbene interaction energies in the triads are larger than those in the dyads, indicating that both the halogen bonding interactions are enhanced. The estimated values of cooperative energy E coop are all negative with much larger E coop in absolute value for the systems including iodine. The nature of halogen bond interactions of the complexes is analyzed using parameters derived from the quantum theory atoms in molecules methodology and energy decomposition analysis. Figure
The structure of NCX?NCX?CH2 complexes (X?=?F, Cl, Br and I) 相似文献
7.
Na Cheng Yongjun Liu Changqiao Zhang Chengbu Liu 《Journal of molecular modeling》2013,19(9):3821-3829
The halogen bonding interactions between C6F5I and a series of transition metal monohalides trans-[M(X)(2-C5NF4)-(PR3)2] (M = Ni, Pd, Pt; X = F, Cl, Br; R = Me, Cy) have been studied with quantum chemical calculations. Optimized geometries of the halogen bonding complexes indicate that angles C1-I···X are basically linear (178–180°) and angles I···X-M mainly range from 90 to 150°. The strength of these metal-influenced halogen bonds alters with different metal centers, metal-bound halogen atoms and the substitutes on phosphine ligands. Electrostatic potential and natural bond orbital analysis show that both of the electrostatic and orbital interactions make a contribution to the formation of halogen bonds, while the electrostatic term plays a dominant role. AIM analysis suggests that, for trans-[M(F)(2-C5NF4)-(PR3)2] (M = Ni, Pd, Pt) monomers, the formed halogen bonding complexes are stabilized by local concentration of the charge of intermediate character, while for the metal monomers containing chlorine and bromine, a typical closed-shell interaction exist. These results prove that the structures and geometries of these halogen bonding complexes can be tuned by changing the halogen atoms and metal centers, which may provide useful information for the design and synthesis of new functional materials. Figure
The properties and structural characteristics of a series of metal-influenced halogen-bonding complexes have been studied by using density functional theory (DFT) method. The calculation results indicate that metal centers and metal-bound halogen atoms have significant influence on the geometries and strength of halogen bonds 相似文献
8.
Jiannan Ji Yanli Zeng Xueying Zhang Shijun Zheng Lingpeng Meng 《Journal of molecular modeling》2013,19(11):4887-4895
The positive electrostatic potentials (σ-hole) have been found in ylides CH2XH3 (X = P, As, Sb) and CH2YH2 (Y = S, Se, Te), on the outer surfaces of group VA and VIA atoms, approximately along the extensions of the C–X and C–Y bonds, respectively. These electrostatic potentials suggest that the above ylides can interact with nucleophiles to form weak, directional noncovalent interactions similar to halogen bonding interactions. MP2 calculations have confirmed the formation of CH2XH3···HM complexes (X = P, As, Sb; M = BeH, ZnH, MgH, Li, Na). The interaction energies, interaction distances, topological properties (electron density and its Laplacian), and energy properties (kinetic electron energy density and potential electron energy density) at the X(1)···H(10) bond critical points are all correlated with the most negative electrostatic potential value of HM, indicating that electrostatic interactions play an important role in these weak X···H interactions. Similar to the halogen bonding interactions, weak interactions involving ylides may be significant in several areas such as organic synthesis, crystal engineering, and design of new materials. 相似文献
9.
Ibrahim MA 《Journal of molecular modeling》2012,18(10):4625-4638
The nature and strength of halogen bonding in halo molecule-Lewis base complexes were studied in terms of molecular mechanics using our recently developed positive extra-point (PEP) approach, in which the σ-hole on the halogen atom is represented by an extra point of positive charge. The contributions of the σ-hole (i.e., positively charged extra point) and the halogen atom to the strength of this noncovalent interaction were clarified using the atomic parameter contribution to the molecular interaction (APCtMI) approach. The molecular mechanical results revealed that the halogen bond is electrostatic and van der Waals in nature, and its strength depends on three types of interaction: (1) the attractive electrostatic interaction between the σ-hole and the Lewis base, (2) the repulsive electrostatic interaction between the negative halogen atom and the Lewis base, and (3) the repulsive/attractive van der Waals interactions between the halogen atom and the Lewis base. The strength of the halogen bond increases with increasing σ-hole size (i.e., magnitude of the extra-point charge) and increasing halogen atom size. The van der Waals interaction's contribution to the halogen bond strength is most favorable in chloro complexes, whereas the electrostatic interaction is dominant in iodo complexes. The idea that the chloromethane molecule can form a halogen bond with a Lewis base was revisited in terms of quantum mechanics and molecular mechanics. Although chloromethane does produce a positive region along the C-Cl axis, basis set superposition error corrected second-order M?ller-Plesset calculations showed that chloromethane-Lewis base complexes are unstable, producing halogen-Lewis base contacts longer than the sum of the van der Waals radii of the halogen and O/N atoms. Molecular mechanics using the APCtMI approach showed that electrostatic interactions between chloromethane and a Lewis base are unfavorable owing to the high negative charge on the chlorine atom, which overcomes the corresponding favorable van der Waals interactions. 相似文献
10.
Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The interaction energy of this interaction varies from a positive value to -90.54 kJ mol(-1) in Al(4)(2-)···I-ethyne-s complex. The interaction strength is affected greatly by the hybridization of C atom and follows the order of C(sp(3)) < C(sp(2)) < C(sp) in most complexes. The methyl group in the halogen donor plays a negative contribution to the formation of halogen bond. The halogen bonding becomes stronger for the heavier halogen atom. The effect of binding site on the strength of halogen bond is related with the nature of halogen atom. The complexes have been analyzed with electrostatic potential, NICS, ELF, NBO, and AIM. 相似文献
11.
Wenjie Wu Yanli Zeng Xiaoyan Li Xueying Zhang Shijun Zheng Lingpeng Meng 《Journal of molecular modeling》2013,19(3):1069-1077
The character of the cooperativity between the HOX···OH/SH halogen bond (XB) and the Y―H···(H)OX hydrogen bond (HB) in OH/SH···HOX···HY (X = Cl, Br; Y = F, Cl, Br) complexes has been investigated by means of second-order Møller?Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. The geometries of the complexes have been determined from the most negative electrostatic potentials (V S,min) and the most positive electrostatic potentials (V S,max) on the electron density contours of the individual species. The greater the V S,max values of HY, the larger the interaction energies of halogen-bonded HOX···OH/SH in the termolecular complexes, indicating that the ability of cooperative effect of hydrogen bond on halogen bond are determined by V S,max of HY. The interaction energies, binding distances, infrared vibrational frequencies, and electron densities ρ at the BCPs of the hydrogen bonds and halogen bonds prove that there is positive cooperativity between these bonds. The potentiation of hydrogen bonds on halogen bonds is greater than that of halogen bonds on hydrogen bonds. QTAIM studies have shown that the halogen bonds and hydrogen bonds are closed-shell noncovalent interactions, and both have greater electrostatic character in the termolecular species compared with the bimolecular species. Figure
The character of the cooperativity between the X···O/S halogen bond (XB) and the Y―H···O hydrogen bond (HB) in OH/SH···HOX···HY (X=Cl, Br; Y=F, Cl, Br) complexes has been investigated by means of second-order Møller—Plesset perturbation theory (MP2) calculations and “quantum theory of atoms in molecules” (QTAIM) studies. 相似文献
12.
The ETS-NOCV analysis was applied to describe the σ-hole in a systematic way in a series of halogen compounds, CF3-X (X?=?I, Br, Cl, F), CH3I, and C(CH3)nH3-n-I (n?=?1,2,3), as well as for the example germanium-based systems. GeXH3, X?=?F, Cl, H. Further, the ETS-NOCV analysis was used to characterize bonding with ammonia for these systems. The results show that the dominating contribution to the deformation density, Δρ 1 , exhibits the negative-value area with a minimum, corresponding to σ-hole. The “size” (spatial extension of negative value) and “depth” (minium value) of the σ-hole varies for different X in CF3-X, and is influenced by the carbon substituents (fluorine atoms, hydrogen atoms, methyl groups). The size and depth of σ-hole decreases in the order: I, Br, Cl, F in CF3-X. In CH3-I and C(CH3)nH3-n-I, compared to CF3-I, introduction of hydrogen atoms and their subsequent replacements by methyl groups lead to the systematic decrease in the σ-hole size and depth. The ETS-NOCV σ-hole picture is consistent with the existence the positive MEP area at the extension of σ-hole generating bond. Finally, the NOCV deformation density contours as well as by the ETS orbital-interaction energy indicate that the σ-hole-based bond with ammonia contains a degree of covalent contribution. In all analyzed systems, it was found that the electrostatic energy is approximately two times larger than the orbital-interaction term, confirming the indisputable role of the electrostatic stabilization in halogen bonding and σ-hole bonding. Figure
Graphical representation of the σ-hole on the halogen atom, based on the molecular electrostatic potential (upper row) and the NOCV deformation-density channel Δρ 1 (lower row and the right-hand side plot) 相似文献
13.
Herbert C. Georg Eudes E. Fileti Thaciana Malaspina 《Journal of molecular modeling》2013,19(1):329-336
Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R = methyl, phenyl, acetyl, H and X = F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX?PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range ?4.14 to ?11.92 kJ mol?1 (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27 % in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl?PH3 and all MeX?PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7–6.7 u.a. (about 3–7 %). 相似文献
14.
The H···π and X (X = F, Cl, Br, I)···π interactions between hypohalous acids and benzene are investigated at the MP2/6-311++G(2d,2p) level. Four hydrogen-bonded
and three halogen-bonded complexes were obtained. Ab initio calculations indicate that the X···π interaction between HOX and
C6H6 is mainly electrostatically driven, and there is nearly an equal contribution from both electrostatic and dispersive energies
in the case of XOH–C6H6 complexes. Natural bond orbital (NBO) analysis reveals that there exists charge transfer from benzene to hypohalous acids.
Atom in molecules (AIM) analysis locates bond critical points (BCP) linking the hydrogen or halogen atom and carbon atom in
benzene. 相似文献
15.
Halogen bonding (XB) is a type of noncovalent interaction between a halogen atom X in one molecule and a negative site in another. X can be chlorine, bromine or iodine. The strength of the interaction increases in the order Cl<Br<I. After a brief review
of experimental evidence relating to halogen bonding, we present an explanation for its occurrence in terms of a region of
positive electrostatic potential that is present on the outermost portions of some covalently-bonded halogen atoms. The existence
and magnitude of this positive region, which we call the σ-hole, depends upon the relative electron-attracting powers of X
and the remainder of its molecule, as well as the degree of sp hybridization of the s unshared electrons of X. The high electronegativity of fluorine and its tendency to undergo significant sp hybridization account for its failure to halogen bond. Some computed XB interaction energies are presented and discussed.
Mention is also made of the importance of halogen bonding in biological systems and processes, and in crystal engineering.
Figure The computed B3PW91/6-31G(d,p) electrostatic potential, in kcal mol−1, on the 0.001 electrons/bohr3 surface of NC–C≡C–Cl. The chlorine atom is at the right. The color ranges are: red, more positive than 15; yellow between 7 and 15; green, between 0 and 7; blue, between −10 and 0; purple, more positive than −10.
Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005. 相似文献
16.
Ramanathan Sangiliapillai Ramdass Arumugam Rajkumar Eswaran Rajagopal Seenivasan 《Luminescence》2016,31(1):30-37
Luminescent heteroleptic ruthenium(II) complexes of type RuLnX3–n [L = 1,10‐phenanthroline (phen), X = 4,7 diphenyl phenanthroline disulfonate, (dpsphen) n = 0,1,2,3] were synthesized and their photophysical properties investigated in homogeneous and cationic (CTAB), anionic (SDS) and nonionic (Triton X‐100) micelles. The luminescent quantum yield and lifetime of the complexes were found to increase in the presence of micellar media and on the introduction of a disulfonate ligand into the coordination sphere. Both electrostatic and hydrophobic interactions play an important role in the micellar media. Thus, by changing the nature of the ligands and the medium, we were able to tune the photophysical properties of Ru(II) complexes. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
17.
Mohamed A. El-Sayed Ahmed H. Abdel Salam Ali El-Dissouky 《Inorganica chimica acta》2004,357(14):4057-4064
Copper(I) halides react quantitatively with piperidine (Pip) in dioxygen-free methylene chloride or nitrobenzene to form tetranuclear copper(I) complexes [(Pip)nCuX]4; n=1 or 2, X=Cl, Br or I. These complexes are very soluble and completely reduce dioxygen to dioxo bridging ligand, with stoichiometry, Δ[Cu(I)]/Δ[O2]=4.0. The stable oxo solids [(Pip)nCuX]4O2 mimic tyrosinase copper protein. They act as a homogeneous oxidative coupling catalysts for phenols. Electronic transition spectra in the near infrared with high molecular absorptivity are diagnostic for tetranuclear “Cu4X4” core structure. The electronic transitions are more likely due to charge transfer between a minimum of three halo ligands and copper(II) center. The room temperature EPR spectra of [(Pip)nCuX]4O2 in methylene chloride are isotropic with four hyperfine lines. The room temperature solid-state EPR spectra of [PipCuX]4O2 show an axial spectra with dx2−y2 ground state, suggesting square pyramidal arrangement of the five coordinated ligands around copper(II) centers. Cyclic voltammetry measurements show that they are more likely irreversible in character and show slight quasi-reversability when X=Br or I. Constant potential electrolysis indicate that the number of electrons consumed are equal to four electrons which will be due to the reduction of four copper(II) to copper(I). 相似文献
18.
The crystal structures of several Pt(II) complexes containing sulfoxide ligands are described. The two iodo bridged dimers of the type I(R2SO)Pt(μ-I)2Pt(R2SO)I (where R is ethyl or n-butyl) are twinned structures. The dinuclear species are the trans isomers. Two compounds of the type trans-Pt(DMSO)(amine)X2 were studied by X-ray diffraction methods. The diiodo MeNH2 compound forms H-bonded chains, formed by maximizing the H-bonds between the amine group with the O atom of DMSO and one iodo ligand. The H-bonding pattern is quite different in the dichloro t-BuNH2 complex. In the latter crystal, there are two independent molecules which are H-bonded in pairs. The methyl groups of DMSO and the t-butyl group of the amine are oriented towards the outside of the pairs of molecules, while the H-bonds link the two independent molecules. Again, the amino group forms the maximum H-bonds with the O atom of DMSO and one chloro ligand. The crystal structures of trans-Pt(DMSO)(pyridine)I2 and of trans-Pt(MeBzSO)(pyrimidine)I2 (Bz = benzyl) were also studied. In the pyridine complex, the O atom of DMSO is in the Pt(II) plane by symmetry, while in the pyrimidine compound, the C atom of the –CH3 group is in the Pt(II) plane. The pyridine and the pyrimidine ligands are perpendicular to the Pt(II) square plane. The trans influence of the different ligands is discussed. 相似文献
19.
William J. Hunks 《Inorganica chimica acta》2006,359(11):3605-3616
The reaction of digold(I) diphosphine complexes [Au2(O2CCF3)2(μ-Ph2P-X-PPh2)] with dithiols HS-Y-SH can give either macrocyclic complexes [Au2(μ-S-Y-S)(μ-Ph2P-X-PPh2)] or polymeric complexes [Au2(μ-S-Y-S)(μ-Ph2P-X-PPh2)]n. The structures of the macrocyclic complex [Au2{μ-(S-4-C6H4)2S}{μ-Ph2P(CH2)4PPh2}], and the polymeric complexes [Aun{μ-(S-CH2CO2CH2CH2O)2-1,4-C6H4}n(μ-trans-Ph2PCHCHPPh2)n] and [Aun{μ-(S-CH2CO2CH2CH2O)2-1,5-C10H6}n(μ-trans-Ph2PCHCHPPh2)n] have been determined. Evidence is presented that the complexes exist primarily as macrocycles in solution and that, in favorable cases, ring-opening polymerization occurs during crystallization. 相似文献
20.
The synthesis of complexes of Li(I), K(I), Mg(II), Ca(II) and Ba(II) with guanosine in basic non aqueous solutions is described. The complexes were of two types: (1) complexes having the general formula, M(Guo)nXm·YH2O·ZC2H5OH, where M = Mg(II), Ca(II), Ba(II) and Li(I), n = 1,2,4, X = Cl?, Br?, NO3?, ClO4? and OH?, m = 1,2, Y = 0?6 and X = 0?2, and (2) complexes with the general formula, M(GuoH-1)(OH)n?1·YH2O, where M = K(I), Ca(Il) and Ba(II), GuoH-1 =Ionized guanosine at N1, n = 1,2 and Y = 1?3. The complexes are characterized by their proton nuclear magnetic resonance (1H NMR) and Fourier transform infrared (FT-IR) spectra. The FT-IR and 1H NMR data of the non ionized nucleoside complexes suggest that the metal binding is through the N7-site of guanine and that the anion (X) is hydrogen bonded to N1H and NH2 groups. In the N1-ionized guanosine complexes the metal binding is via the O6? of guanine. All the complexes formed exhibited a transition of the sugar conformation from C2′-endo/anti in the free nucleoside to C3′-endo/anti in the metal complexes. 相似文献