1-乙基-3-甲基咪唑阳离子与天冬酰胺阴离子的相互作用

利用密度泛函理论B3LYP方法, 在6-311+G(d,p)水平上, 对1-乙基-3-甲基咪唑阳离子[Emim]+与天冬酰胺阴离子[Asn]-形成的氨基酸离子液体气态阴阳离子对([Emim][Asn])进行理论研究. 通过几何结构优化和频率分析得到势能面上的五个稳定构型. [Emim]+和[Asn]-之间能够形成较强的氢键相互作用, 零点能校正后的能量在-373.96至-326.28 kJ·mol-1之间. 其稳定化能主要来源于[Asn]-中羰基O的孤对电子lp(O)与[Emim]+中C—H反键轨道σ*(C—H)之间的相互作用: lp(O)→σ*(C—H). 红外光谱特征和自然布居分析(NPA)计算表明咪唑阳离子中参与形成氢键的C—H键振动的红移值、阴阳离子间的电荷转移与氢键相互作用能成正比关系. 分子中的原子(AIM)理论分析得到[Emim]+和[Asn]-之间的氢键相互作用以静电作用为主. 通过计算结果初步探讨影响氨基酸离子液体玻璃化温度Tg的结构因素.     

Stabilities of ion/radical adducts in the liquid phase as derived from the dependence of electrochemical cleavage reactivities upon solvent.

The idea that significant ion/radical interactions should vary with solvent if they do exist in the liquid phase was pursued by an investigation of the dissociative electron-transfer reactivity of carbon tetrachloride and 4-cyanobenzyl chloride in four different solvents, 1,2-dichloroethane, N,N-dimethylformamide, ethanol, and formamide, by means of their cyclic voltammetric responses. Modification of the conventional dissociative electron transfer theory to take account of an interaction between fragments in the ion/radical pair resulting from the dissociative electron reaction allows a satisfactory fitting of the experimental data leading to the determination of the interaction energy. There is an approximate correlation between the interaction energies in the ion/radical pair and the solvation free energies of the leaving anion, Cl(-). The interaction is maximal in 1,2-dichloroethane, which is both the least polar and the least able to solvate Cl(-). The interaction is smaller in the polar solvents, albeit distinctly measurable. The two protic solvents, ethanol and formamide, which are the most able to solvate Cl(-), give rise to similar interaction energies. The interaction is definitely stronger in N,N-dimethylformamide, which has a lesser ability to solvate Cl(-) than the two other polar solvents. The existence of significant ion/radical interactions in polar media is thus confirmed and a route to their determination opened.     

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.     

分子动力学模拟研究[Bmim][PF_6]+水+醇三元体系的微观结构和分子间相互作用(英文)

研究离子液体体系的微观结构和分子间相互作用具有重要意义.本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF6])+水+乙醇和[Bmim][PF6]+水+异丙醇三元体系进行了分子模拟研究,计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能,并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能.在此基础上,研究了溶液体系的微观结构、分子间相互作用和相行为.结果表明,水倾向于与离子液体阴离子和阳离子极性部分作用,醇倾向于与阴离子和阳离子非极性部分作用;库仑力主导阴离子-溶剂相互作用,色散力主导阳离子-溶剂相互作用,阴阳离子的缔合状态对色散力影响较小,对库仑力的影响非常显著.     

The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

Summary A new simple empirical function has been developed that estimates the free energy of binding for a given protein-ligand complex of known 3D structure. The function takes into account hydrogen bonds, ionic interactions, the lipophilic protein-ligand contact surface and the number of rotatable bonds in the ligand. The dataset for the calibration of the function consists of 45 protein-ligand complexes. The new energy function reproduces the binding constants (ranging from 2.5·10^-2 to 4·10^-14 M, corresponding to binding energies between -9 and -76 kJ/mol) of the dataset with a standard deviation of 7.9 kJ/mol, corresponding to 1.4 orders of magnitude in binding affinity. The individual contributions to protein-ligand binding obtained from the scoring function are: ideal neutral hydrogen bond: -4.7 kJ/mol; ideal ionic interaction: -8.3 kJ/mol; lipophilic contact: -0.17 kJ/mol Ų; one rotatable bond in the ligand: +1.4 kJ/mol. The function also contains a constant contribution (+5.4 kJ/mol) which may be rationalized as loss of translational and rotational entropy. The function can be evaluated very fast and is therefore also suitable for application in a 3D database search or de novo ligand design program such as LUDI.     

Origin of attraction, magnitude, and directionality of interactions in benzene complexes with pyridinium cations

Geometries and interaction energies of benzene complexes with pyridine, pyridinium, N-methylpyridinium were studied by ab initio molecular orbital calculations. Estimated CCSD(T) interaction energies of the complexes at the basis set limit were -3.04, -14.77, and -9.36 kcal/mol, respectively. The interactions in the pyridinium and N-methylpyridinium complexes should be categorized into a cation/pi interaction, because the electrostatic and induction interactions greatly contribute to the attraction. On the other hand, the interaction in the pyridine complex is a pi/pi interaction. The dispersion interaction is mainly responsible for the attraction in the benzene-pyridine complex. Short-range interactions including charge-transfer interactions are not important for the attraction in the three complexes. The most stable pyridinium complex has a T-shaped structure, in which the N-H bond points toward the benzene, while the N-methylpyridinium complex prefers a slipped-parallel structure. The benzene-pyridine complex has two nearly isoenergetic (Slipped-parallel and T-shaped) structures.     

Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes

Using basis‐set extrapolation schemes for a given data set, we evaluated the binding energies and geometries at the complete basis set (CBS) limit at the levels of the second order Møller–Plesset perturbation theory (MP2) and the coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)]. The systems include the hydrogen bonding (water dimer), aromatic interaction (benzene dimer), π–H interaction (benzene–water), cation–water, anion–water, π–cation interaction (cation–benzene), and π–anion interaction (anion–triazine). One extrapolation method is to exploit both BSSE‐corrected and BSSE‐uncorrected binding energies for the aug‐cc‐pVNZ (N = 2, 3, 4, …) basis set in consideration that both binding energies give the same CBS limit (CBS^B). Another CBS limit (CBS^C) is to use the commonly known extrapolation approach to exploit that the electron correlation energy is proportional to N^?3. Since both methods are complementary, they are useful for estimating the errors and trend of the asymptotic values. There is no significant difference between both methods. Overall, the values of CBS^C are found to be robust because of their consistency. However, for small N (in particular, for N = 2, 3), CBS is found to be slightly better for water–water interactions and cation–water and cation–benzene interactions, whereas CBS is found to be more reliable for bezene–water and anion–water interactions. We also note that the MP2 CBS limit value based on N = 2 and 3 combined with the difference between CCSD(T) and MP2 at N = 2 would be exploited to obtain a CCSD(T)/CBS value for aromatic–aromatic interactions and anion–π interactions, but not for cationic complexes. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008     

Solvation effect of guest, supramolecular host, and host-guest compounds on the thermodynamic selectivity of calix(4)arene derivatives and soft metal cations

This paper reports thermodynamic data for the transfer of calixarene derivatives and their metal-ion complexes in dipolar aprotic solvents. These data are used to assess the effect of solvation of these compounds on the selective complexation shown by these macrocycles for soft metal cations in different media. Thus, solubilities and derived Gibbs energies of solution of 5,11,17,23-tetra-tert-butyl[25,27-bis(hydroxyl)-26,28-bis(ethylthioethoxy)]calix(4)arene, 1, and 5,11,17,23-tetra-tert-butyl-[25,27-bis(ethylenethanoate)-26,28-bis(ethylthioethoxy)]-calix(4)arene, 2, in various solvents at 298.15 K are reported. Solvation of these ligands in one medium relative to another is analyzed from their standard transfer Gibbs energies using acetonitrile as the reference solvent. These data are combined with transfer enthalpies (derived from standard solution enthalpies obtained calorimetrically) to calculate the corresponding entropies of transfer of these calix(4)arene derivatives from acetonitrile to methanol and N,N-dimethylformamide. As far as the metal-ion salts (silver and mercury) in their free and complex forms are concerned, standard solution enthalpies were determined in acetonitrile, methanol, and N,N-dimethylformamide. These data are used to derive their transfer enthalpies from one medium to another. It is concluded that the extent of complexation of these macrocycles with soft metal cations is controlled by not only the solvation changes that the free cation undergoes in moving from one medium to another but also those for the ligand and its complex cation in these solvents.     

Ab initio interaction energies of hydrogen-bonded amino acid side chain[bond]nucleic acid base interactions

Hydrogen-bonding interactions often make substantial contributions to the specificity of protein-nucleic acid complexes. Using a geometric modeling approach, we previously identified 28 possible doubly hydrogen-bonded interactions to the four unpaired RNA bases. Here we present interaction energies of these models, calculated by ab initio quantum chemical methods, and describe a correlation between the computed energies and observed frequencies of the interactions. In general, interactions with charged side chains show the most favorable energies. An Asp/Glu-G interaction may be especially favorable for recognition of unpaired guanines in RNAs. Asn and Ser/Thr/Tyr side chains are calculated to make iso-energetic interactions to the Hoogsteen face of adenine, but Asn-A interactions are much more common with DNA than RNA, and Ser/Thr/Tyr-A interactions are more common with RNA than DNA. Examination of the known interactions suggests that Ser/Thr/Tyr may be accommodated in a wider variety of protein contexts at RNA-protein interfaces. With these calculated intrinsic affinities, it should be possible to better assess the contributions of bidentate hydrogen-bonding interactions to RNA- and DNA-binding specificity.     

分子动力学模拟研究[Bmim][PF6]+水+醇三元体系的微观结构和分子间相互作用

研究离子液体体系的微观结构和分子间相互作用具有重要意义. 本文对1-丁基-3-甲基咪唑六氟磷酸盐([Bmim][PF₆])+水+乙醇和[Bmim][PF₆]+水+异丙醇三元体系进行了分子模拟研究, 计算了径向分布函数和不同组成的水-醇混合溶剂与离子液体阴阳离子间的相互作用能, 并将其分解为库仑相互作用能和Lennard-Jones(LJ)势能. 在此基础上, 研究了溶液体系的微观结构、分子间相互作用和相行为. 结果表明, 水倾向于与离子液体阴离子和阳离子极性部分作用, 醇倾向于与阴离子和阳离子非极性部分作用; 库仑力主导阴离子-溶剂相互作用, 色散力主导阳离子-溶剂相互作用, 阴阳离子的缔合状态对色散力影响较小, 对库仑力的影响非常显著.     

Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches

Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of residue types to be separated by a certain spatial distance or to have a given relative orientation. Several such potentials, describing different kinds of correlations between residue types, distances, and orientations, are derived and combined in a way that maximizes their information content and minimizes their redundancy. To test the ability of these potentials to describe cation-pi and amino-pi systems, we compare their energies with those computed with the CHARMM molecular mechanics force field and with quantum chemistry calculations at the Hartree-Fock level (HF) and at the second order of the M?ller-Plesset perturbation theory (MP2). The latter calculations are performed in the gas phase and in acetone, in order to mimic the average dielectric constant of protein environments. The energies computed with the best of our statistical potentials and with gas-phase HF or MP2 show correlation coefficients up to 0.96 when considering one side-chain degree of freedom in the statistical potentials and up to 0.94 when using a totally simplified model excluding all side-chain degrees of freedom. These potentials perform as well as, or better than, the CHARMM molecular mechanics force field that uses a much more detailed protein representation. The good performance of our cation-pi statistical potentials suggests their utility in protein structure and stability prediction and in protein design.     

Continuum solvation models in the linear interaction energy method

The linear interaction energy (LIE) method in combination with two different continuum solvent models has been applied to calculate protein-ligand binding free energies for a set of inhibitors against the malarial aspartic protease plasmepsin II. Ligand-water interaction energies are calculated from both Poisson-Boltzmann (PB) and Generalized Born (GB) continuum models using snapshots from explicit solvent simulations of the ligand and protein-ligand complex. These are compared to explicit solvent calculations, and we find close agreement between the explicit water and PB solvation models. The GB model overestimates the change in solvation energy, and this is caused by consistent underestimation of the effective Born radii in the protein-ligand complex. The explicit solvent LIE calculations and LIE-PB, with our standard parametrization, reproduce absolute experimental binding free energies with an average unsigned error of 0.5 and 0.7 kcal/mol, respectively. The LIE-GB method, however, requires a constant offset to approach the same level of accuracy.     

Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer

The observation of short halogen-carbonyl oxygen interactions in protein-ligand complexes has spurred us to use computational tools to better understand the strength of halogen bonding interactions. In this study we have produced potential energy curves for the halogen bonding interactions of several halobenzene-formaldehyde complexes. It was found that, for most halogen substituents, a halobenzene and formaldehyde form stable halogen bonded complexes with interaction energies that increase as the size of the halogen substituent increases.     

A theoretical investigation of the interaction between small Pd particles and 1-butyl-3-methyl imidazolium ionic liquids with Cl(-), BF(4)(-) and PF(6)(-) anions

Density functional calculations have been used to investigate the interaction between Pd(n) clusters (n = 1-6) and 1-butyl-3-methylimidazolium (Bmim(+)) based ionic liquids (ILs) with the anions [Cl(-)], [BF(4)(-)] and [PF(6)(-)]. The interaction of small Pd(n) clusters (1 ≤ n ≤ 6) with a single cation or anion is also studied. The interaction strengths in anion-Pd(n) categories with n = 1-6 follow the trend [Cl(-)] > [BF(4)(-)] > [PF(6)(-)]. The cation could also form interactions with Pd(n) clusters. Compared with a single anion or cation, the interaction could be strengthened when palladium particles interact with the whole ion pair. Further studies indicated that anionPd interaction is the decisive factor in the interaction between the Pd atom and the whole ion pair. The Pd(2) dimer interacts with the whole ion pair much more strongly than the Pd atom. Solvent effects have been considered in the present study by means of the polarizable continuum model. It is found that the stability of [Bmim(+)·BF(4)(-)]-Pd(n) and [Bmim(+)·PF(6)(-)]-Pd(n) complexes with n = 1 and 2 can be improved in solvents.     

Theoretical study of adsorption of sarin and soman on tetrahedral edge clay mineral fragments

This study provides details of the structure and interactions of Sarin and Soman with edge tetrahedral fragments of clay minerals. The adsorption mechanism of Sarin and Soman on these mineral fragments containing the Si(4+) and Al(3+) central cations was investigated. The calculations were performed using the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. The studied systems were fully optimized. Optimized geometries, adsorption energies, and Gibbs free energies of Sarin and Soman adsorption complexes were computed. The number and strength of formed intermolecular interactions have been analyzed using the AIM theory. The charge of the systems and a termination of the mineral fragment are the main contributing factors on the formation of intermolecular interactions in the studied systems. In the neutral complexes, Sarin and Soman is physisorbed on these mineral fragments due to the formation of C-H...O, and O-H...O hydrogen bonds. The chemical bond is formed between a phosphorus atom of Sarin and Soman and an oxygen atom of the -2 charged clusters containing an Al(3+) central cation and -1 charged complex containing a Si(4+) central cation (chemisorption). Sarin and Soman interact mostly in the same way with the same terminated edge mineral fragments containing different central cations. However, the interaction energies of the complexes with an Al(3+) central cation are larger than these values for the Si(4+) complexes. The interaction enthalpies of all studied systems corrected for the basis set superposition error were found to be negative. However, on the basis of the Gibbs free energy values, only strongly interacting complexes containing a charged edge mineral fragment with an Al(3+) central cation are stable at room temperature. We can conclude that Sarin and Soman will be adsorbed preferably on this type of edge mineral surfaces. Moreover, on the basis of the character of these edge surfaces, a tetrahedral edge mineral fragment can provide effective centers for the dissociation.     

The remarkably invariant interaction energies of lithium first-row compounds with water and with ammonia

Solvation energies of lithium first-row compounds LiX (X ? H, Li, BeH, BH₂, CH₃, NH₂, OH, F) and of the lithium cation with the model solvents, water and ammonia, have been calculated ab inito (MP2/6-31 + G^*//6-31G^* with zero-point vibrational energy corrections at 3-21G//3-21G). The solvation energies are found to be remarkably constant: ?18.0 ± 1.2 and ?21.5 ± 1.3 kcal/mol for the hydrates and ammonia solvates, respectively. This independence on the nature of X is due largely to the ionic character of the LiX compounds (dipole moments 4.7–6.6 debye). The unexpectedly high solvation energies of the lithium molecule (?14.3 and ?17.8 kcal/mol, respectively) are due to the polarizability of Li₂. At the same level, the lithium cation has interaction energies with H₂O and NH₃ of ?34.1 and ?39.7 kcal/mol, respectively. For the hydrates of LiOH and LiF cyclic structures with hydrogen bonds and somewhat increased solvation energies also are described.     

Experimental and Theoretical Insights into the Optical Properties and Intermolecular Interactions in Push-Pull Bromide Salts

Experimental and theoretical insights into the nature of intermolecular interactions and their effect on optical properties of 1-allyl-4-(1-cyano-2-(4-dialkylaminophenyl)vinyl)pyridin-1-ium bromide salts ( I and II ) are reported. A comparison of optical properties in solution and in the solid-state of the salts ( I and II ) with their precursors ( Ia and IIa ) is made. The experimental absorption maxima (λ_max) in CHCl₃ is at 528 nm for I and at 542 nm for II , and a strong bathochromic shift of ∼110 nm is observed for salts I and II compared with their precursors. The absorption bands in solid-state at ∼627 nm for I and at ∼615 nm for II that are assigned to charge transfer (CT) effect. The optical properties and single crystal structural features of I and II are explored by experimental and computational tools. The calculated λ_max and the CT are in good agreement with the experimental results. The intermolecular interactions existing in the crystal structures and their energies are quantified for various dimers by PIXEL, QTAIM and DFT approaches. Three types of interactions, (i) the cation⋅⋅⋅cation interactions, (ii) cation⋅⋅⋅anion interactions and (iii) anion⋅⋅⋅anion interactions are observed. The cationic moiety is mainly destabilized by C−H⋅⋅⋅N/π and π⋅⋅⋅π interactions whereas the cation and anion moiety is predominantly stabilized by strong C−H⋅⋅⋅Br⁻ interactions in both structures. The existence of charge transfer between cation and anion moieties in these structures is established through NBO analysis.     

A theoretical study of the effect of a tetraalkylammonium counterion on the hydrogen bond strength in Z-hydrogen maleate.

High-level ab initio calculations (B3LYP/6-31+G and QCISD(T)/6-311+G**) were carried out to resolve the disagreement between recent experimental and computational estimates of the relative strength of the intramolecular hydrogen bond in Z-hydrogen maleate anion with respect to the normal hydrogen bond in maleic acid. The computational estimates for the strength of the intramolecular hydrogen bond in the gas-phase maleate anion are in a range of 14-28 kcal/mol depending on the choice of the reference structure. Computational data suggest that the electrostatic influence of a counterion such as a tetraalkylammonium cation can considerably weaken the hydrogen bonding interaction (by 1.5-2 times) in the complexed hydrogen maleate anion relative to that in the naked anion. The estimated internal H-bonding energies for a series of Z-maleate/R4N+ salts (R = CH3, C2H5, CH3CH2CH2CH2) range from 8 to 13 kcal/mol. The calculated energy differences between the E- and Z-hydrogen maleates complexed to Me4N+, Et4N+, and Bu4N+ cation are 4.9 (B3LYP/6-31+G(d,p)) and 5.7 and 5.8 kcal/mol (B3LYP/6-31G(d)). It is also demonstrated that the sodium cation exerts a similar electrostatic influence on the hydrogen bond strength in bifluoride anion (FHF-). The present study shows that while low-barrier short hydrogen bonds can exist in the gas phase (the barrier for the hydrogen transfer in maleate anion is only 0.2 kcal/mol at the QCISD(T)/6-311+G//QCISD/6-31+G level), whether they can also be strong in condensed media or not depends on how their interactions with their immediate environment affect their strength.     

A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.