Binding free energy, energy and entropy calculations using simple model systems

Free energy differences are calculated for a set of two model host molecules, binding acetone and methanol. Two active sites of different characteristics were constructed based on an artificially extended C60 fullerene molecule, possibly functionalised to include polar interactions in an otherwise apolar, spherical cavity. The model host systems minimise the necessary sampling of conformational space while still capturing key aspects of ligand binding. The estimates of the free energies are split up into energetic and entropic contributions, using three different approaches investigating the convergence behaviour. For these systems, a direct calculation of the total energy and entropy is more efficient than calculating the entropy from the temperature dependence of the free energy or from a direct thermodynamic integration formulation. Furthermore, the compensating surrounding–surrounding energies and entropies are split off by calculating reduced ligand-surrounding energies and entropies. These converge much more readily and lead to properties that are more straightforwardly interpreted in terms of molecular interactions and configurations. Even though not experimentally accessible, the reduced thermodynamic properties may prove highly relevant for computational drug design, as they may give direct insights into possibilities to further optimise ligand binding while optimisation in the surrounding–surrounding energy or entropy will exactly cancel and not lead to improved affinity.     

Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

Relative free energy calculations based on molecular dynamics simulations are combined with available experimental binding free energies to predict unknown binding affinities of acyclic Cucurbituril complexes in the blind SAMPL3 competition. The predictions yield root mean square errors between 2.6 and 3.2 kcal/mol for seven host-guest systems. Those deviations are comparable to results for solvation free energies of small organic molecules. However, the standard deviations found in our simulations range from 0.4 to 2.4 kcal/mol, which indicates the need for better sampling. Three different approaches are compared. Bennett's Acceptance Ratio Method and thermodynamic integration based on the trapezoidal rule with 12 λ-points exhibit a root mean square error of 2.6 kcal/mol, while thermodynamic integration with Simpson's rule and 11 λ-points leads to a root mean square error of 3.2 kcal/mol. In terms of absolute median errors, Bennett's Acceptance Ratio Method performs better than thermodynamic integration with the trapezoidal rule (1.7 vs. 2.9 kcal/mol). Simulations of the deprotonated forms of the guest molecules exhibit a poorer correspondence to experimental results with a root mean square error of 5.2 kcal/mol. In addition, a decrease of the buffer concentration by approximately 20 mM in the simulations raises the root mean square error to 3.8 kcal/mol.     

Efficient calculation of SAMPL4 hydration free energies using OMEGA,SZYBKI, QUACPAC,and Zap TK

Several submissions for the SAMPL4 hydration free energy set were calculated using OpenEye tools, including many that were among the top performing submissions. All of our best submissions used AM1BCC charges and Poisson–Boltzmann solvation. Three submissions used a single conformer for calculating the hydration free energy and all performed very well with mean unsigned errors ranging from 0.94 to 1.08 kcal/mol. These calculations were very fast, only requiring 0.5–2.0 s per molecule. We observed that our two single-conformer methodologies have different types of failure cases and that these differences could be exploited for determining when the methods are likely to have substantial errors.     

Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD,and SMD solvation models

We applied the solvation models SM8, SM8AD, and SMD in combination with the Minnesota M06-2X density functional to predict vacuum-water transfer free energies (Task 1) and tautomeric ratios in aqueous solution (Task 2) for the SAMPL2 test set. The bulk-electrostatic contribution to the free energy of solvation is treated as follows: SM8 employs the generalized Born model with the Coulomb field approximation, SM8AD employs the generalized Born approximation with asymmetric descreening, and SMD solves the nonhomogeneous Poisson equation. The non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell is treated as a sum of terms that are products of geometry-dependent atomic surface tensions and solvent-accessible surface areas of the individual atoms of the solute. On average, three models tested in the present work perform similarly. In particular, we achieved mean unsigned errors of 1.3 (SM8), 2.0 (SM8AD), and 2.6 kcal/mol (SMD) for the aqueous free energies of 30 out of 31 compounds with known reference data involved in Task 1 and mean unsigned errors of 2.7 (SM8), 1.8 (SM8AD), and 2.4 kcal/mol (SMD) in the free energy differences (tautomeric ratios) for 21 tautomeric pairs in aqueous solution involved in Task 2.     

Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge

We present our predictions for the SAMPL4 hydration free energy challenge. Extensive all-atom Monte Carlo simulations were employed to sample the compounds in explicit solvent. While the focus of our study was to demonstrate well-converged and reproducible free energies, we attempted to address the deficiencies in the general Amber force field force field with a simple QM/MM correction. We show that by using multiple independent simulations, including different starting configurations, and enhanced sampling with parallel tempering, we can obtain well converged hydration free energies. Additional analysis using dihedral angle distributions, torsion-root mean square deviation plots and thermodynamic cycles support this assertion. We obtain a mean absolute deviation of 1.7 kcal mol^?1 and a Kendall’s τ of 0.65 compared with experiment.     

Predicting octanol/water partition coefficients for the SAMPL6 challenge using the SM12, SM8, and SMD solvation models

Journal of Computer-Aided Molecular Design - Blind predictions of octanol/water partition coefficients at 298 K for 11 kinase inhibitor fragment like compounds were made for the SAMPL6 challenge....     

7,7-二甲基-2-对溴苯基-4-苯基-5-氧代-1,4,5,6,7,8-六氢化-6H-喹啉的合成及晶体结构

标题化合物C23H22BrNO是由1-(4-溴苯基)-3-苯基-2-丙烯-1-酮与5,5-二甲基-1, 3-环己二酮在N, N-二甲基甲酰胺(DMF)中在NH4OAc催化下反应而得。结构通过单晶X-射线衍射分析确定,其晶体属于单斜晶系,空间群C2/C, a = 19.678(4),b = 13.571(2),c = 17.311(3) 牛琤 = 118.74(1),Mr = 408.33, V = 4055(1) ?,Dc = 1.338 g/cm3, Z = 8, m (MoKa) = 2.038 mm-1, F(000) = 1680, R = 0.0539,wR = 0.1369。X-衍射分析表明,六元环C(10)C(13)C(16)C(17)采用半椅式构象:原子C(10),C(11),C(12),C(16)和C(17)在同一个平面内,而原子C(13)远离平面为0.3282 牛闷矫嬗?个苯环的夹角分别为41.09, 81.97,2个苯环的夹角为75.87。另外在晶体结构中,存在1个分子间氢键。     

Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models

Journal of Computer-Aided Molecular Design - Blind predictions of octanol/water partition coefficients and pKa at 298.15 K for 22 drug-like compounds were made for the SAMPL7 challenge....     

Indolizines. 6. Relative reactivities of isomeric 6-, 7-, and 8-ethoxycarbonylindolizine derivatives

The kinetics of the alkaline hydrolysis of 2-phenyl-6-, -7-, and -8-ethoxycarbonylindolizines were studied. The rate constants for the hydrolysis of these compounds and the indexes of the dissociation constants of 2-phenylindolizine-6-,-7-, and -8-carboxylic acids were determined by spectrophotometry. The indexes of the electronic structures and reactivities of 2-methyl-6-, -7-, and -8-ethoxycarbonylindolizines were calculated from theory.See [1] for Communication [5].Deceased.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 5, pp. 627–633, May, 1979.     

Enantiospecific synthesis of (6R,7S,8aR)-dihydroxyindolizidine and (6R,7R,8S,8aR)-trihydroxyindolizidine from D-glucose.

Enantiospecific syntheses of (6R,7S,8aR)-dihydroxyindolizidine (1) and (6R,7R,8S,8aR)-trihydroxyindolizidine (2) from readily available methyl 2-azido-4,6-O-benzylidene-2-deoxy-α-D-altropyranoside (5) are described.     

Homodimerization of neurotensin 1 receptor involves helices 1, 2, and 4: insights from quaternary structure predictions and dimerization free energy estimations

A computational approach based upon rigid-body docking, ad hoc filtering, and cluster analysis has been combined with a protocol for dimerization free energy estimations to predict likely interfaces in the neurotensin 1 receptor (NTS1) homodimers. The results of this study suggest that the likely intermonomer interfaces compatible with in vitro binding affinity constants essentially involve helices 1, 2, and 4 and do not include disulfide bridges. The correlative model initially developed on Glycophorin A and herein extended to a G protein-Coupled Receptor (GPCR) appears to be a useful tool for estimating the association free energies of transmembrane proteins independent of the size and shape of the interface. In the desirable future cases, in which in vitro intermonomer binding affinities will be available for other GPCRs, such a correlative model will work as an additional criterion for helping in the selection of the most likely dimers.     

3,3,6,6-四甲基-4a-羟基-9-邻甲氧基苯基-1,8-二氧代-2,3,4,4a,5,6,7,8,9,9a-十氢化-1H-氧杂蒽的合成和晶体结构

标题化合物C24H30O5是由邻甲氧基苯甲醛与5，5-二甲基-1，3-环己二酮在N，N-二甲基甲酰胺中反应而得。结构通过单晶X-射线衍射法确定，其晶体属于单斜晶系，空间群C2／c，a=33．942（6），b=7273（1），c=22667（4）A，β=128．989（9）°，Mr=398．50，V=4349（1）A3，Dc=1．2179·cm-3，Z=8，μ（MoKa）=840mm－1，F（000）=1712。晶体结构用直接法解出，经用全矩阵最小二乘法对原子参数进行修正，最后的偏离因子为R=0.043，Rw=0．052。在晶体结构中，存在一个分子间氢键。     

A Chemical Study of Burley Tobacco Flavour (Nicotiana tabacumL.) V. Identification and Synthesis of the Novel Terpenoid Alkaloids 1, 3, 6, 6-Tetramethyl-5, 6, 7, 8-tetrahydro-isoquinolin-8-one and 3, 6, 6-Trimethyl-5,6-dihydro-7H-2-pyrindin-7-one

GLC. allowed the isolation of 1, 3, 6, 6-tetramethyl-5, 6, 7, 8-tetrahydro-isoquinolin-8-one (A) and 3,6,6-trimethyl-5,6-dihydro-7H-2-pyrindin-7-one (D) from Burley tobacco condensate (about 0.1% each). The structures and syntheses of these novel terpenoid alkaloids are described, and a possible way for their formation in tobacco is suggested.     

A convenient synthesis of 6-, 7-, and 8-membered cyclic phosphodiesters

1,3-, 1,4-, and 1,5-Alkanediols are converted into the corresponding 6-, 7-, and 8- membered cyclic phosphodiesters in a two-step procedure utilizing N-(1,2-dimethylethylene-dioxyphosphoryl)imidazole ($\text{2}\text{?}$ as the sole phosphorylating reagent.     

A (1,3) Strain in cis- and trans-5, 6-dihydro-4, 6-dimethyl-4H, 8H-pyrido [3,2,1-de]phenanthridin-8-ones

The stereochemistry of trans- and cis-2, 4-dimethyl-tetrahydroquinolines, 6 and 7 were derived from ¹H-NMR. studies. These were converted respectively into trans- and cis-5, 6-dihydro-4, 6-dimethyl-4H, 8H-pyrido [3, 2, 1-de]phenanthridin-8-ones 18 and 20 by a Pschorr reaction on the anthranilamides 10 and 15 . Bromophenanthridones 19 and 21 were similarly prepared from bromoanthranilamides 12 and 17 . Detailed ¹H-NMR. studies on 18 and 20 indicated axial disposition of the methyl groups at C(2) in both compounds in contrast to the situation in 6 and 7 . This is presumably to avoid adverse CH₃CO group interaction of the A (1, 3) type. The severity of this is gauged by the preference of 20 for a normally forbidding 1, 3-diaxial orientation of two methyl groups. X-ray crystallographic studies on 19 and 20 confirm the stereochemical assignments.     

Convergence and error estimation in free energy calculations using the weighted histogram analysis method

The weighted histogram analysis method (WHAM) has become the standard technique for the analysis of umbrella sampling simulations. In this article, we address the challenges (1) of obtaining fast and accurate solutions of the coupled nonlinear WHAM equations, (2) of quantifying the statistical errors of the resulting free energies, (3) of diagnosing possible systematic errors, and (4) of optimally allocating of the computational resources. Traditionally, the WHAM equations are solved by a fixed-point direct iteration method, despite poor convergence and possible numerical inaccuracies in the solutions. Here, we instead solve the mathematically equivalent problem of maximizing a target likelihood function, by using superlinear numerical optimization algorithms with a significantly faster convergence rate. To estimate the statistical errors in one-dimensional free energy profiles obtained from WHAM, we note that for densely spaced umbrella windows with harmonic biasing potentials, the WHAM free energy profile can be approximated by a coarse-grained free energy obtained by integrating the mean restraining forces. The statistical errors of the coarse-grained free energies can be estimated straightforwardly and then used for the WHAM results. A generalization to multidimensional WHAM is described. We also propose two simple statistical criteria to test the consistency between the histograms of adjacent umbrella windows, which help identify inadequate sampling and hysteresis in the degrees of freedom orthogonal to the reaction coordinate. Together, the estimates of the statistical errors and the diagnostics of inconsistencies in the potentials of mean force provide a basis for the efficient allocation of computational resources in free energy simulations.     

Asymmetric synthesis of anthracyclinones using chiral acetal: synthesis of a new chiral AB-synthon, ()-2-bromo-6-ethynyl-6-hydroxy-5, 6, 7, 8-tetrahydro-1, 4-naphthoquinone,and its application for ()-7-deoxydaunomycinone

A synthesis of a new chiral AB-synthon (4) for preparing the optically active anthracyclinones was attained through a stereospecific nucleophilic addition of trimethylsilylethynylmagnesium chloride to the chiral 2-tetralone-1-acetal (2). Synthesis of ()-7-deoxydaunomycinone (1c) was achieved by a regiospecific cycloaddition of4 to 4-acetoxy-8-methoxyhomophthalic anhydride (5).