Halogen bonding in ligand-receptor systems in the framework of classical force fields

Halogen bond is an important non-covalent interaction which is receiving a growing attention in the study of protein-ligand complexes. Many drugs are halogenated molecules and it has been recently shown that many halogenated ligands establish halogen bonds with biomolecules. As the halogen bond nature is due to an anisotropy of the electrostatic potential around halogen atoms, it is not possible to use traditional force fields based on a set of atom-centred charges to study halogen bonds in biomolecules. We show that the introduction of pseudo-atoms on halogens permits us to correctly describe the anisotropy of the electrostatic potential and to perform molecular dynamics simulations on complexes of proteins with halogenated ligands that reproduce experimental values. The results are compared with crystallographic data and with hybrid quantum mechanics/molecular mechanics calculations.     

Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds

A class II valence force field covering a broad range of organic molecules has been derived employing ab initio quantum mechanical "observables." The procedure includes selecting representative molecules and molecular structures, and systematically sampling their energy surfaces as described by energies and energy first and second derivatives with respect to molecular deformations. In this article the procedure for fitting the force field parameters to these energies and energy derivatives is briefly reviewed. The application of the methodology to the derivation of a class II quantum mechanical force field (QMFF) for 32 organic functional groups is then described. A training set of 400 molecules spanning the 32 functional groups was used to parameterize the force field. The molecular families comprising the functional groups and, within each family, the torsional angles used to sample different conformers, are described. The number of stationary points (equilibria and transition states) for these molecules is given for each functional group. This set contains 1324 stationary structures, with 718 minimum energy structures and 606 transition states. The quality of the fit to the quantum data is gauged based on the deviations between the ab initio and force field energies and energy derivatives. The accuracy with which the QMFF reproduces the ab initio molecular bond lengths, bond angles, torsional angles, vibrational frequencies, and conformational energies is then given for each functional group. Consistently good accuracy is found for these computed properties for the various types of molecules. This demonstrates that the methodology is broadly applicable for the derivation of force field parameters across widely differing types of molecular structures. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1782-1800, 2001     

Structures and stabilities of group 13 adducts [(NHC)(EX3)] and [(NHC)2(E2X(n))] (E=B to In; X=H, Cl; n=4, 2, 0; NHC=N-heterocyclic carbene) and the search for hydrogen storage systems: a theoretical study

Quantum chemical calculations using density functional theory at the BP86/TZVPP level and ab initio calculations at the SCS-MP2/TZVPP level have been carried out for the group 13 complexes [(NHC)(EX(3))] and [(NHC)(2)(E(2)X(n))] (E=B to In; X=H, Cl; n=4, 2, 0; NHC=N-heterocyclic carbene). The monodentate Lewis acids EX(3) and the bidentate Lewis acids E(2) X(n) bind N-heterocyclic carbenes rather strongly in donor-acceptor complexes [(NHC)(EX(3))] and [(NHC)(2)(E(2)X(n))]. The equilibrium structures of the bidentate complexes depend on the electronic reference state of E(2)X(n), which may vary for different atoms E and X. All complexes [(NHC)(2)(E(2)X(4))] possess C(s) symmetry in which the NHC ligands bind in a trans conformation to the group 13 atoms E. The complexes [(NHC)(2)(E(2)H(2))] with E=B, Al, Ga have also C(s) symmetry with a trans arrangement of the NHC ligands and a planar CE(H)E(H)C moiety that has a E=E π bond. In contrast, the indium complex [(NHC)(2)(In(2) H(2))] has C(i) symmetry with pyramidal-coordinated In atoms in which the hydrogen atoms are twisted above and below the CInInC plane. The latter C(i) form is calculated for all chloride systems [(NHC)(2)(E(2)Cl(2))], but the boron complex [(NHC)(2)(B(2)Cl(2))] deviates only slightly from C(s) symmetry. The B(2) fragment in the linear coordinated complex [(NHC)(2)(B(2))] has a highly excited (3)(1)Σ(g)(-) reference state, which gives an effective B≡B triple bond with a very short interatomic distance. The heavier homologues [(NHC)(2)(E(2))] (E=Al to In) exhibit a anti-periplanar arrangement of the NHC ligands in which the E(2) fragments have a (1)(1) Δ(g) reference state and an E=E double bond. The calculated energies suggest that the dihydrogen release from the complexes [(NHC)(EH(3))] and [(NHC)(2)(E(2)H(n))] becomes energetically more favourable when atom E becomes heavier. The indium complexes should therefore be the best candidates of the investigated series for hydrogen-storage systems that could potentially deliver dihydrogen at close to ambient temperature. The hydrogenation reaction of the dimeric magnesium(I) compound [LMgMgL] (L=β-diketiminate) with [(NHC)(EH(3))] becomes increasingly exothermic with the trend B相似文献   

Steric effects in the aerobic oxidation of pi-allylnickel(II) complexes with N-heterocyclic carbenes

Pi-allylchloro(NHC)nickel(II) complexes were synthesized and their reactions with O2 were studied. Ligand steric effects were found to determine the difference between rapid oxidation of the allyl group to produce bis-mu-hydroxonickel complexes and no observable reaction. The ability of the metal-NHC bond to rotate correlates with the ability of the complex to react with O2. In the limiting cases, conformationally restricted complexes are stable to O2 and complexes with rapid Ni-NHC bond rotation react rapidly with O2. Complexes with intermediate conformational flexibility were found to exhibit lesser reactivity with O2. On the basis of the observed inertness of complexes with saddle-shaped ligands to O2, we propose the adoption of a nonplanar geometry upon reaction with O2 to be required. The issue of conformational flexibility versus rigidity is expected to directly impact the catalytic behavior of metal-NHC complexes.     

A combined magnetic circular dichroism and density functional theory approach for the elucidation of electronic structure and bonding in three- and four-coordinate iron(ii)–N-heterocyclic carbene complexes

Iron salts and N-heterocyclic carbene (NHC) ligands is a highly effective combination in catalysis, with observed catalytic activities being highly dependent on the nature of the NHC ligand. Detailed spectroscopic and electronic structure studies have been performed on both three- and four-coordinate iron(ii)–NHC complexes using a combined magnetic circular dichroism (MCD) and density functional theory (DFT) approach that provide detailed insight into the relative ligation properties of NHCs compared to traditional phosphine and amine ligands as well as the effects of NHC backbone structural variations on iron(ii)–NHC bonding. Near-infrared MCD studies indicate that 10Dq(T _d) for (NHC)₂FeCl₂ complexes is intermediate between those for comparable amine and phosphine complexes, demonstrating that such iron(ii)–NHC and iron(ii)–phosphine complexes are not simply analogues of one another. Theoretical studies including charge decomposition analysis indicate that the NHC ligands are slightly stronger donor ligands than phosphines but also result in significant weakening of the Fe–Cl bonds compared to phosphine and amine ligands. The net result is significant differences in the d orbital energies in four-coordinate (NHC)₂FeCl₂ complexes relative to the comparable phosphine complexes, where such electronic structure differences are likely a significant contributing factor to the differing catalytic performances observed with these ligands. Furthermore, Mössbauer, MCD and DFT studies of the effects of NHC backbone structure variations (i.e. saturated, unsaturated, chlorinated) on iron–NHC bonding and electronic structure in both three- and four-coordinate iron(ii)–NHC complexes indicate only small differences as a function of backbone structure, that are likely amplified at lower oxidation states of iron due to the resulting decrease in the energy separation between the occupied iron d orbitals and the unoccupied NHC π* orbitals.     

Study of peptide conformation in terms of the ABEEM/MM method

The ABEEM/MM model (atom-bond electronegativity equalization method fused into molecular mechanics) is applied to study of the polypeptide conformations. The Lennard-Jones and torsional parameters were optimized to be consistent with the ABEEM/MM fluctuating charge electrostatic potential. The hydrogen bond was specially treated with an electrostatic fitting function. Molecular dipole moments, dimerization energies, and hydrogen bond lengths of complexes are reasonably achieved by our model, compared to ab initio results. The ABEEM/MM fluctuating charge model reproduces both the peptide conformational energies and structures with satisfactory accuracy with low computer cost. The transferability is tested by applying the parameters of our model to the tetrapeptide of alanine and another four dipeptides. The overall RMS deviations in conformational energies and key dihedral angles for four di- or tetrapeptide, is 0.39 kcal/mol and 7.7 degrees . The current results agree well with those by the accurate ab initio method, and are comparable to those from the best existing force fields. The results make us believe that our fluctuating charge model can obtain more promising results in protein and macromolecular modeling with good accuracy but less computer cost.     

Piano-Stool Ruthenium N-Heterocyclic Carbene Complexes for gem-Specific Catalytic Dimerization of Terminal Alkynes

A series of piano-stool Ru−NHC (NHC=N-heterocyclic carbene) complexes have been prepared and characterized. The NHC ligands used herein have varying wingtip groups, showing the impact of steric congestion on the selectivity for the catalytic dimerization of terminal alkynes.     

Application of torsion angle molecular dynamics for efficient sampling of protein conformations

We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency.     

Pd-N-杂环卡宾化合物催化的Heck反应、Suzuki反应进展

Pd催化的C—C键偶联反应是形成碳—碳单键的重要反应之一.传统上,使用膦化合物为配体来调整催化活性及选择性.但大多数Pd-膦化合物对空气稳定性差,容易被氧化;在溶液中易于解离出膦配体而降低催化剂稳定性,通常需要给反应体系中加入较多的膦配体以保持催化剂的稳定性和活性.1991年发现的稳定N-杂环卡宾(NHC)类配体具有富含电子、给电子能力强,对金属配位能力强,结构易修饰等特点,使得金属-NHC化合物成为金属有机化学、催化等领域研究新的焦点.Pd-NHC化合物已经可催化多类有机反应,是继传统Pd-膦催化剂外的又一类高效催化剂.综述了近年来不同结构的NHC如单齿简单NHC、双齿NHC、含其它配位原子的NHC等配体与Pd的配合物在Heck反应、Suzuki反应等偶联反应中的应用.     

Interpreting protein structural dynamics from NMR chemical shifts

In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical shift predictions generally improve agreement with experimental values when compared to predictions made from static X-ray structures. Improved chemical shift predictions result from population-weighted sampling of multiple conformational states and from sampling smaller fluctuations within conformational basins. Improved chemical shift predictions also result from discrete changes to conformations observed in X-ray structures, which may result from crystal contacts, and are not always reflective of conformational dynamics in solution. Chemical shifts are sensitive reporters of fluctuations in backbone and side chain torsional angles, and averaged (1)H chemical shifts are particularly sensitive reporters of fluctuations in aromatic ring positions and geometries of hydrogen bonds. In addition, poor predictions of MD-averaged chemical shifts can identify spurious conformations and motions observed in MD simulations that may result from force field deficiencies or insufficient sampling and can also suggest subsets of conformational space that are more consistent with experimental data. These results suggest that the analysis of dynamically averaged NMR chemical shifts from MD simulations can serve as a powerful approach for characterizing protein motions in atomistic detail.     

单嘧磺隆晶体-活性构象转换的分子动力学模拟

应用分子动力学模拟方法对单嘧磺隆在水、正辛醇和正辛烷3种不同溶剂中的构象行为、单嘧磺隆与3种溶剂之间的相互作用能及氢键相互作用进行了计算研究. 计算结果表明, 在3种不同的溶剂中, 单嘧磺隆的优势构象不同; 其构象转换过程, 特别是转换成活性构象的过程主要发生在水溶液中; 与溶剂分子间的相互作用是分子构象行为的决定因素; 单嘧磺隆的脲桥部分可以和含氢键接受体的溶剂形成氢键, 分子间与分子内氢键的竞争可能是从晶体构象转换成活性构象的主要驱动力.     

Theoretical study of complexes of extended cyclopentadienyl ligands with zinc and cadmium

Using density functional theory, we have theoretically studied various kinds of complexes of cyclopentadienyl and dicyclopentadienyl ligands with zinc and cadmium atoms of oxidation state +1. We first find that a sandwich complex Cp-Zn-Zn-Cp that was recently identified by Resta et al, (Science 2004, 305, 1136) has a large overall binding energy (=-3.19 eV), where Cp denotes the pentamethyl cyclopentadienyl group. In addition, Cp-Zn-Zn-Cp is found to have a binding energy even larger by 0.93 eV, where Cp is a cyclopentadienyl ligand without methyl groups attached. Electronic structure analysis shows accumulation of electron density between Zn atoms, confirming the existence of Zn-Zn bond that is as strong as typical transition metal-halide bonds. In addition, our calculation suggests the possible existence of similar complexes Cp-Zn-Cd-Cp and Cp-Zn-Cd-Cp with a Zn-Cd bond not known thus far. Furthermore, study on the dimetallic complexes of dicyclopentadienyl ligands also predicts results which hold potential application to organometallic chemistry and organic synthesis: (a) Complexes involving a stiff ligand Dp can presumably exist in the form of dimerized sandwich complexes Dp-2M(1)-2M(2)-Dp (M(1), M(2) = Zn, Cd) with two metal-metal bonds. Their overall binding energies amount to -1.84 to -3.48 eV depending upon the kinds of metallic atoms, the strongest binding corresponding to dizinc complex. (b) Complexes involving more flexible ligand Ep can also form similar sandwich complexes Ep-2M(1)-2M(2)-Ep, but with much larger overall binding energies (=-4.97 to -7.09 eV). In addition, they can also exist in the form of nonsandwich complexes M(1)-Ep-M(2) involving only one ligand. Unlike most of dimetallic complexes of other transition metals, syn conformations are found to be exceptionally stable due to the formation of M(1)-M(2) bonds. Careful electronic structure analysis gives deep insight into the nature of observed phenomena.     

Conformational sensitivity analysis of FKBP–FK506/rapamycin complexes

Sensitivity analysis techniques are applied to the FKBP–FK506 and FKBP–rapamycin complexes to quantify the conformational relationships between FKBP and its ligands. Crystal structures of the two FKBP complexes are energy minimized in the Amber force field using a continuum solvent model, and derived Green's function sensitivity coefficients are developed to describe the relationship between the ?, ψ, and χ₁ torsional angles of the FKBP residues and the bound ligand macrocycle torsional angles. Sensitivity analysis is applied to the entire FKBP structure and reveals that the local conformation of the residues of the 80s and 50s loops and of the active site are sensitive to the ligand conformation. The analysis also reveals that the torsional angles controlling the orientation of the amide and keto carbonyls of FK506 are sensitive to the aromatic side chains in the FKBP carbonyl binding pocket. © 1994 by John Wiley & Sons, Inc.     

Molecular dynamics simulation of cellobiose in water

The conformational behavior of cellobiose was studied by molecular dynamics simulation in a periodic box of waters. Several different initial conformations were used and the results compared with equivalent vacuum simulations. The average positions and rms fluctuations within single torsional conformations of cellobiose were affected only slightly by the solvent. However, water damped local torsional librations and transitions. The conformational energies of the solute and their fluctuations were also sensitive to the presence of solvent. Intramolecular hydrogen bonding was weakened relative to that observed in vacuo due to competition with solvating waters. All cellobiose hydroxyl groups participated in intermolecular hydrogen bonds with water, with approximately eight hydrogen bonds formed per glucose ring. The hydrogen bonding was predominantly between water hydrogens and solute hydroxyl oxygens. Intermolecular hydrogen bonding to ring and bridge oxygens was seldom present. The diffusion coefficients of both water and solute agree closely with experimental values. Water interchanged rapidly between the solvating first shell and the bulk on the picosecond time scale. © 1993 John Wiley & Sons, Inc.     

The Development of Bulky Palladium NHC Complexes for the Most-Challenging Cross-Coupling Reactions

Palladium‐catalyzed cross‐coupling reactions enable organic chemists to form C? C bonds in targeted positions and under mild conditions. Although phosphine ligands have been intensively researched, in the search for even better cross‐coupling catalysts attention has recently turned to the use of N‐heterocyclic carbene (NHC) ligands, which form a strong bond to the palladium center. PEPPSI (pyridine‐enhanced precatalyst preparation, stabilization, and initiation) palladium precatalysts with bulky NHC ligands have established themselves as successful alternatives to palladium phosphine complexes. This Review shows the success of these species in Suzuki–Miyaura, Negishi, and Stille–Migita cross‐couplings as well as in amination and sulfination reactions.     

Mechanistic Study of Pd/NHC-Catalyzed Sonogashira Reaction: Discovery of NHC-Ethynyl Coupling Process

The product of a revealed transformation—NHC-ethynyl coupling—was observed as a catalyst transformation pathway in the Sonogashira cross-coupling, catalyzed by Pd/NHC complexes. The 2-ethynylated azolium salt was isolated in individual form and fully characterized, including X-ray analysis. A number of possible intermediates of this transformation with common formulae (NHC)_nPd(C₂Ph) (n=1,2) were observed and subjected to collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) experiments to elucidate their structure. Measured bond dissociation energies (BDEs) and IRMPD spectra were in an excellent agreement with quantum calculations for coupling product π-complexes with Pd⁰. Molecular dynamics simulations confirmed the observed multiple CID fragmentation pathways. An unconventional methodology to study catalyst evolution suggests the reported transformation to be considered in the development of new catalytic systems for alkyne functionalization reactions.     

Structural and models of dioxouranium(VI) with rhodanine azodyes--V.

The synthesis of several new coordination compounds of dioxouranium(VI) heterochelates with bidentate rhodanineazol compounds derived from rhodanine are described. The ligands and uranyl complexes have been charcaterized by various physico-chemical techniques. The bond lengths and the force constants have been calculated from asymmetric stretching frequency of O-U-O group. The infrared spectral studies showed a monobasic bidentate behaviour with the oxygen and azonitrogen donor system. The ligands contain intramolecular hydrogen bonds.     

Dinuclear PdII complexes bearing mixed NHC/Py/PPh3 donor set ligands: Catalytic applications and electrochemical investigations

Bimetallic palladium(II) complexes containing classical NHC donor ligands are becoming increasingly popular owing to their various catalytic applications. However, examples of the aforementioned complexes with mixed NHC/PPh₃ ligands are still rare. Bimetallic palladium(II) complexes possessing these mixed ligands are described starting from a C2-symmetric bis-imidazolium salt containing 4,4′-substituted central biphenyl ring. All the palladium(II) complexes have been tested as precatalysts in α-arylation of oxindole and Suzuki–Miyaura coupling reactions. The complex composed of mixed NHC/PPh₃ donor ligands shows superior catalytic activity compared with the corresponding PEPPSI type complexes when applied in α-arylation of oxindole. The dinuclear complexes display better activity compared with the mononuclear complexes. The preliminary electrochemical measurements show the facile oxidation of Pd^II in the presence of combined NHC/PPh₃ ligands compared with a combination of NHC/Py ligands.     

Palladium–N-heterocyclic carbene complexes for the Mizoroki–Heck reaction: An appraisal

This article presents a review of the most significant developments with N-heterocyclic carbene (NHC)–palladium catalytic systems used for the Heck reaction. For more than the past two decades, a large number of new NHC–Pd complexes have been synthesized and characterized. These studies focused on NHCs as a phosphine analogue, but the current review highlights the differences with particular ligands so as to attain a suitable balance between the electronic and bulky environments around the metal. NHCs have gained wide recognition as these ligands act as excellent σ-donors that form stable metal–NHCs with strong metal–carbon bonds. For this reason, metal–NHCs are commonly used as they are highly reactive and can selectively serve as catalysts for various chemical transformations. The objective of our article is to highlight significant recent progress in NHC–Pd(II) complexes and provide an overview of their extensive interaction in the Mizoroki–Heck reaction.     

Conformational analysis of hydroxymatairesinol in aqueous solution with molecular dynamics

Molecular dynamics simulations were performed on the naturally occuring lignan hydroxymatairesinol (HMR) using the GROMACS software. The aim of this study was to explore the conformational behavior of HMR in aqueous solution adopting the TIP4P model. The topology of HMR was constructed by hand and HMR was modeled with the OPLS‐AA force field implemented in GROMACS. The five torsional angles in HMR were properly analyzed during the simulations. Correlations through certain patterns were observed between the angles. The determining property for the conformation preferred in aqueous solution was found to be the dipole moment and not the lowest energy in gas phase. The solvation effects on HMR was also studied by quantum chemical calculations applying the COnductorlike Screening MOdel (COSMO), the results of which were compared with results from a previous study using the Polarized Continuum Model (PCM). In the present work, COSMO was found to give more credible relative energies than PCM. © 2009 Wiley Periodicals, Inc., J Comput Chem, 2009