Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

We used molecular dynamics simulation and free energy perturbation (FEP) methods to investigate the hydride-ion transfer step in the mechanism for the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of a novel substrate by the enzyme dihydrofolate reductase (DHFR). The system is represented by a coupled quantum mechanical and molecular mechanical (QM/MM) model based on the AM1 semiempirical molecular orbital method for the reacting substrate and NADPH cofactor fragments, the AMBER force field for DHFR, and the TIP3P model for solvent water. The FEP calculations were performed for a number of choices for the QM system. The substrate, 8-methylpterin, was treated quantum mechanically in all the calculations, while the larger cofactor molecule was partitioned into various QM and MM regions with the addition of “link” atoms (F, CH₃, and H). Calculations were also carried out with the entire NADPH molecule treated by QM. The free energies of reaction and the net charges on the NADPH fragments were used to determine the most appropriate QM/MM model. The hydride-ion transfer was also carried out over several FEP pathways, and the QM and QM/MM component free energies thus calculated were found to be state functions (i.e., independent of pathway). A ca. 10 kcal/mol increase in free energy for the hydride-ion transfer with an activation barrier of ca. 30 kcal/mol was calculated. The increase in free energy on the hydride-ion transfer arose largely from the QM/MM component. Analysis of the QM/MM energy components suggests that, although a number of charged residues may contribute to the free energy change through long-range electrostatic interactions, the only interaction that can account for the 10 kcal/mol increase in free energy is the hydrogen bond between the carboxylate side chain of Glu30 (avian DHFR) and the activated (protonated) substrate. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 977–988, 1998     

Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods

The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method combined with alanine-scanning mutagenesis is a very important tool for rational drug design. In this study, molecular dynamics (MD) and MM-PBSA were applied to calculate the binding free energy between the rat intestinal fatty acid binding protein (IFABP) and palmitic acid (PA) to gain insight to the interaction details. Equally spaced snapshots along the trajectory were chosen to perform the binding free energy calculation, which yields a result highly consistent with experimental value with a deviation of 0.4 kcal/mol. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in IFABP to alanine and recomputing the DeltaDeltaG(binding). By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated DeltaDeltaG(binding) is below 1.5 kcal/mol for most of the alanine mutations of the noncharged residues (67% in total). To further investigate some particular mutants, three additional dynamical simulations of IFABP Arg126Ala, Arg106Ala, and Arg106Gln mutants were conducted. Recalculated binding free energies are well consistent with the experimental data. Moreover, the ambiguous role of Arg106 caused by the free energy change of the opposite sign when it is mutated to alanine and glutamine respectively is clarified both structurally and energetically. Typically, this can be attributed to the partial electrostatic compensation mainly from Arg56 and the obvious entropy gain in Arg106Ala mutant while not in Arg106Gln mutant. The presented structural model of IFABP-PA complex could be used to guide future studies.     

Theoretical insight into structural and electronic properties of cationic Scn+ (n=2-13): A benchmark study

Geometric, thermodynamic and electronic properties of cationic scandium clusters are studied. Geometric optimizations and stable spin states of Sc₂⁺ are assessed on high level ab-initio coupled cluster method CCSD(T) with different dunning correlation consistent basis sets (aug-cc-pVDZ, aug-cc-pVTZ and aug-cc-pVQZ). Then, 23 DFT functionals belonging to different classes are evaluated at 6-31G (d), LANL2MB, LANL2DZ and Def2-SVP basis sets, and the results are compared with the benchmarked coupled cluster calculations. Due to excellent correlation, PBEPBE/LANL2DZ was chosen to perform calculation of higher scandium cationic clusters Sc_n⁺ (n = 3-13). In addition, we explored relative stability, binding energies, second order energy differences, vertical ionization energies, vertical electron affinities and HOMO-LUMO gaps. Moreover, these results are also compared with the neutral scandium clusters.     

LANL2DZ basis sets recontracted in the framework of density functional theory

In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.     

Computational alanine scanning mutagenesis--an improved methodological approach

Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (DeltaDeltaG(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations.     

杯[4]吡咯-阴离子体系相互作用的理论研究——杯[4]吡咯-卤素阴离子体系的密度泛函研究

用密度泛函B3LYP/LANL2DZ方法对自由杯[4]吡咯的最低能量构象和卤素阴离子-杯[4]吡咯复合物进行了计算研究.结果表明,杯[4]吡咯与卤素离子能通过彼此间的相互作用形成复合物,并且这种相互作用在本质上应为分子间的氢键相互作用;杯[4]吡咯与卤素阴离子形成的复合物在构型变化、电荷转移、前线轨道及其作用方式、成键布居以及能量和热力学参数等方面均按元素周期律有规律地变化,杯[4]吡咯与卤素阴离子间的相互作用沿元素周期依次减少.     

Study of Hg22+ and complexes of NpO2+ and UO22+ in solution. examples of cation-cation interactions

Density functional theory (BPW91/TZ2P) is used to explore the nature of cation-cation interactions (CCIs) that exist between two actinyl cations in solution. Solvation, which is modeled using COSMO, favors the complexes (ONpO-ONpO)2+ and (ONpO-OUO)3+ over separated NpO2+(aq) and UO2(2+)(aq) cations because of the quadratic dependence of solvation on charge. For (OUO-OUO)4+, solvation effects, even though very large, are unable to overcome intrinsic electrostatic repulsion between the units. The actinyl-actinyl complexes are T-shaped, with the oxygen of one unit coordinated to the actinide metal of the other unit. The association free energies of (ONpO-ONpO)2+ and (ONpO-OUO)3+ are calculated as -42.1 and -29.2 kcal/mol. Explicit consideration of the first solvation shell at the B3LYP/LANL2DZ level suggests that the free energies of binding may be overestimated. The Hg2(2+) dication, though not considered a "traditional" CCI, is very similar to the actinyl-actinyl interaction. The binding free energy of Hg2(2+) in solution is calculated as -16.0 kcal/mol.     

Theoretical study of [Li(H2O)n]+ and [K(H2O)n]+ (n = 1−4) complexes

The geometries, successive binding energies, vibrational frequencies, and infrared intensities are calculated for the [Li(H₂O)_n]⁺ and [K(H₂O)_n]⁺ (n = 1?4) complexes. The basis sets used are 6-31G* and LANL 1DZ (Los Alamos ECP +DZ ) at the SCF and MP 2 levels. There is an agreement for calculated structures and frequencies between the MP 2/6-31G* and MP 2/LANL 1DZ basis sets, which indicates that the latter can be used for calculations of water complexes with heavier ions. Our results are in a reasonable agreement with available experimental data and facilitate experimental study of these complexes. © 1995 John Wiley & Sons, Inc.     

二茂铁及其衍生物的电化学特性与结构理论研究

研究了二茂铁及其衍生物(甲酰二茂铁,乙酰二茂铁,甲醇二茂铁和乙酸二茂铁)的电化学行为,运用结构理论给出了二茂铁D5点群群轨道能级图与二茂铁衍生物的前线轨道能级图,得出在二茂铁分子结构中1e2(dx2-y2,dxy)与3a1(dz2,4s)分别属于分子前线轨道中的HOMO和LUMO。同时用密度泛函理论(DFT)在LANL2DZ基组水平上对其结构进行了全优化,得到了二茂铁及其衍生物前线最高被占轨道(HOMO)能量值,Fe原子净电荷,对其电化学行为与前线轨道能级相对大小进行了验证。     

A molecular dynamics investigation on the interaction properties of AzrC and its cofactor

In this report, the main contributions of FMN were employed in the reductive cleavage reaction of AzrC protein (as a member of azoreductase family). Molecular dynamics simulations of three models in the presence and absence of FMN and ligand were performed to gather information about the dynamic nature of active site residues of AzrC. Combination of pairwise decomposition and alanine scanning calculations provides critical information about the FMN binding sites. The MD results analyzed by alanine scanning method revealed the high negative scores for N 10 (A) A, N 12 (A) A, S 17 (A) A and Y 151 (A) A mutations, which were in agreement with pairwise decomposition analyses. Hydrogen bond analyses indicated that these residues play critical roles in establishing appropriate hydrogen bonds between AzrC and FMN. Negative energy results for nonpolar residues such as W 103 (A), M 102 (A) and F 105 (A) and binding free energy analyses of three complexes indicate that the VDW interactions could be regarded as some favorable contribution in FMN and AzrC protein and confirmed the critical role of FMN in ligand binding (35.84 %), in addition to its catalytic function. This information could be used for future experimental investigations.     

Theoretical study on the spectroscopic properties and electronic structures of heteroleptic phosphorescent Ir(III) complexes

The geometries, spectroscopic and electronic structures properties of a series of heteroleptic phosphorescent Ir(III) complexes including N981, N982, N983, N984 have been characterized by density functional theory calculations. The excited‐state properties of the Ir(III) complexes have been characterized by CIS method. The ground‐ and excited‐state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. By using the time‐dependent density functional theory method, the absorption and phosphorescence spectra were calculated based on the optimized ground‐ and excited‐state geometries, respectively. The results show that the absorption and emission data agree well with the corresponding experimental results. The calculated results also revealed that the nature of the substituent at the 4‐position of the pyridyl moiety can influence the distributions of HOMO and LUMO and their energies. In addition, the charge transport quality has been estimated approximately by the calculated reorganization energy (λ). Our result also indicates that the positions of the substitute groups not only change the transition characters but also affect the charge transfer rate and balance, and complex N982 is a very good charge transfer material for green OLEDs. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces

In the context of protein-protein interactions, the term "hot spot" refers to a residue or cluster of residues that makes a major contribution to the binding free energy, as determined by alanine scanning mutagenesis. In contrast, in pharmaceutical research, a hot spot is a site on a target protein that has high propensity for ligand binding and hence is potentially important for drug discovery. Here we examine the relationship between these two hot spot concepts by comparing alanine scanning data for a set of 15 proteins with results from mapping the protein surfaces for sites that can bind fragment-sized small molecules. We find the two types of hot spots are largely complementary; the residues protruding into hot spot regions identified by computational mapping or experimental fragment screening are almost always themselves hot spot residues as defined by alanine scanning experiments. Conversely, a residue that is found by alanine scanning to contribute little to binding rarely interacts with hot spot regions on the partner protein identified by fragment mapping. In spite of the strong correlation between the two hot spot concepts, they fundamentally differ, however. In particular, while identification of a hot spot by alanine scanning establishes the potential to generate substantial interaction energy with a binding partner, there are additional topological requirements to be a hot spot for small molecule binding. Hence, only a minority of hot spots identified by alanine scanning represent sites that are potentially useful for small inhibitor binding, and it is this subset that is identified by experimental or computational fragment screening.     

Computational alanine scanning of the 1:1 human growth hormone-receptor complex

The MM-PBSA (Molecular Mechanics-Poisson-Boltzmann surface area) method was applied to the human Growth Hormone (hGH) complexed with its receptor to assess both the validity and the limitations of the computational alanine scanning approach. A 400-ps dynamical trajectory of the fully solvated complex was simulated at 300 K in a 101 A x 81 A x 107 A water box using periodic boundary conditions. Long-range electrostatic interactions were treated with the particle mesh Ewald (PME) summation method. Equally spaced snapshots along the trajectory were chosen to compute the binding free energy using a continuum solvation model to calculate the electrostatic desolvation free energy and a solvent-accessible surface area approach to treat the nonpolar solvation free energy. Computational alanine scanning was performed on the same set of snapshots by mutating the residues in the structural epitope of the hormone and the receptor to alanine and recomputing the deltaGbinding. To further investigate a particular structure, a 200-ps dynamical trajectory of an R43A hormone-receptor complex was simulated. By postprocessing a single trajectory of the wild-type complex, the average unsigned error of our calculated deltadeltaGbinding is approximately1 kcal/mol for the alanine mutations of hydrophobic residues and polar/charged residues without buried salt bridges. When residues involved in buried salt bridges are mutated to alanine, it is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results. Our approach can be extended to rapid screening of a variety of possible modifications to binding sites.     

Copper(II) and cobalt(II) complexes of 2,6-diacetylpyridine bis(<Emphasis Type="Italic">O</Emphasis>-methyloxime): A theoretical investigation

The molecular geometries and vibrational frequencies of the title compounds in the ground state are calculated using the Hartree-Fock (HF) and density functional theory (DFT/B3LYP) methods with the LANL2DZ basis set and compared with the experimental data. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies show good agreement with the experimental values. The energetic behavior of the title compounds in solvent media is examined using the B3LYP method with the LANL2DZ basis set by applying the Onsager and polarizable continuum model (PCM). In addition, molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analyses of the title compounds are investigated by theoretical calculations.     

Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between inhibitors and protein variants. In this article, the importance of hydrophobic and hydrophilic residues to the binding of adenosine monophosphate (AMP) to the fructose 1,6-bisphosphatase (FBPase), a target enzyme for type-II diabetes, was examined by FEP method. Five mutations were made to the FBPase enzyme with AMP inhibitor bound: 113Tyr --> 113Phe, 31Thr --> 31Ala, 31Thr --> 31Ser, 177Met --> 177Ala, and 30Leu --> 30Phe. These mutations test the strength of hydrogen bonds and van der Waals interactions between the ligand and enzyme. The calculated relative free energies indicated that: 113Tyr and 31Thr play an important role, each via two hydrogen bonds affecting the binding affinity of inhibitor AMP to FBPase, and any changes in these hydrogen bonds due to mutations on the protein will have significant effect on the binding affinity of AMP to FBPase, consistent to experimental results. Also, the free energy calculations clearly show that the hydrophilic interactions are more important than the hydrophobic interactions of the binding pocket of FBPase.     

氢甲酰化反应溶剂效应的量子化学研究

在B3LYP/6-31G(d, p)(Rh和P采用LANL2DZ + Polar)水平下,利用自洽反应场（SCRF）的Onsager模型,系统研究了C6H12、C6H6、THF、CH2Cl2、CH3OH和H2O（相对介电常数ε分别为2.02、2.25、7.58、8.93、32.63和78.39）六种溶剂对乙烯氢甲酰化反应中各驻点的结构和反应机理的影响.分别在上述溶剂中优化了反应物、产物、中间体和过渡态的结构,并计算了自由能和活化自由能.计算结果表明,不同溶剂对反应势能面上各驻点的结构和能量均有一定的影响,而且随着相对介电常数ε的增加,反应的活化自由能下降.水是以上六种溶剂中最佳的溶剂,这与大量的实验研究结果一致.     

Density functional calculation of the structure and electronic properties of Cu(n)O(n) (n = 1-8) clusters

Ab initio simulations and calculations were used to study the structures and stabilities of copper oxide clusters, Cu(n)O(n) (n = 1-8). The lowest energy structures of neutral and charged copper oxide clusters were determined using primarily the B3LYP/LANL2DZ model chemistry. For n ≥ 4, the clusters are nonplanar. Selected electronic properties including atomization energies, ionization energies, electron affinities, and Bader charges were calculated and examined as a function of n.     

Theoretical study on the influence of ancillary ligand on the spectroscopic properties and electronic structures of phosphorescent Pt(II) complexes

The geometries, energies, and electronic properties of a series of phosphorescent Pt(II) complexes including FPt, CFPt, COFPt, and NFPt have been characterized within density functional theory DFT calculations which can reproduce and rationalize experimental results. The properties of excited‐states of the Pt(II) complexes were characterized by configuration interaction with singles (CIS) method. The ground‐ and excited‐state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. In addition, we also have performed a triplet UB3LYP optimization for complex FPt and compared it with CIS method in the emission properties. The datum (562.52 nm) of emission wavelength for complex FPt, which were computed based on the triplet UB3LYP optimization excited‐state geometry, is not agreement with the experiment value (500 nm). The absorption and phosphorescence wavelengths were computed based on the optimized ground‐ and excited‐state geometries, respectively, by the time‐dependent density functional theory (TD‐DFT) methods. The results revealed that the nature of the substituent at the phenylpyridine ligand can influence the distributions of HOMO and LUMO and their energies. Moreover, the auxiliary ligand pyridyltetrazole can make the molecular structure present a solid geometry. In addition, the charge transport quality has been estimated approximately by the predicted reorganization energy (λ). Our result also indicates that the substitute groups and different auxiliary ligand not only change the nature of transition but also affect the rate and balance of charge transfer. By summarizing the results, we can conclude that the NFPt is good OLED materials with a solid geometry and a balanced charge transfer rate. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

谷氨酰胺结合蛋白的分子动力学模拟和自由能计算

谷氨酰胺结合蛋白(Glutamine-binding protein, GlnBp)是大肠杆菌透性酶系统中一个细胞外液底物专一性结合蛋白, 对于细胞外液中谷氨酰胺(Gln)的运输和传递至关重要. 本文运用分子动力学(Molecular dynamics, MD)模拟采样, 考察了GlnBp关键残基与底物Gln之间的相互作用和GlnBp两条铰链的功能差别; 并采用MM-PBSA方法计算了GlnBp与底物Gln的结合自由能. 结果表明: Ph13, Phe50, Thr118和Ile69与底物Gln的范德华相互作用和Arg75, Thr70, Asp157, Gly68, Lys115, Ala67, His156与底物Gln的静电相互作用是结合Gln的主要推动力; 复合物的铰链区85～89柔性大, 对构象开合提供了结构基础; 而铰链区181～185柔性小, 其作用更多是在功能上把底物Gln限制在口袋中; 自由能预测值与实验值吻合. 本研究很好地解释了GlnBp结构与功能的关系, 为进一步了解GlnBp的开合及转运Gln的机制提供了重要的结构信息.     

On the rhodanines and their presence in biologically active ligands

An innovative use of cluster analysis is presented to compare the output from different levels of theory. A dendrogram shows the relative energies of the tautomers of methylidene rhodanine (5-methylene-2-thioxo-thiazolidin-4-one), computed by the semiempirical molecular orbital method AM1, are remarkably similar to the ab initio values from the LANL2DZ++(d,p) basis set, which involves effective core potentials augmented by polarization and diffuse functions. However, the optimized bond lengths and bond angles at the AM1 and AM1/SM1 levels do not agree well with those obtained at the 6–31G^* and LANL2DZ++(d,p) levels of theory or with experiment. Database searching is used to obtain an indication of how common the rhodanine ring is. The prevalence of rhodanine-containing compounds of pharmaceutical interest is very small despite the fact that the compounds exhibit a wide variety of bioactivity.