A complete shape characterization for molecular charge densities represented by Gaussian-type functions

An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented, tested and applied for a family of AB₂ molecules. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend continuously on two parameters: a density value defining the density contour, and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is modeled by means of Gaussian-type functions. The method employs an explicit form of the charge density function in order to compute the curvature properties for the molecular surfaces analytically, from which the shape groups are derived by the algorithm. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visual inspection of the results of the shape analysis is a possible option. For a given molecule, in a given nuclear configuration, the technique provides a two-dimensional shape map, displaying the distribution of shape groups as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis of shape maps automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, several two-dimensional shape maps for simple systems are discussed. The changes induced in these maps by a change in the nuclear geometry, as well as by the changes of the nuclear charge, are also analyzed. The method is applicable to large biomolecules of interest if charge density information is available.     

(Z)-1,2-二苯基-1,3-丁二烯与单取代的乙烯衍生物区位选择性环加成反应

(Z)-1,2-二苯基-1,3-丁二烯分别与甲基乙烯基酮、丙烯酰胺、丙烯腈以及丙烯醛发生环加成反应,均生成顺式和反式的连位取代环己烯衍生物。以IR、¹HNMR和MS鉴定了产物的结构。利用CNDO/2法计算了分子轨道能量和系数,由前线分子轨道理论解释了这种环加成反应的区位选择性。     

A comparison of various MO methods for predicting regioselectivity in Diels-Alder reactions

Various semiempirical MO methods for predicting regioselectivity in Diels-Alder reactions are compared in order to examine their reliability. They are the frontier molecular orbital method using CNDO/2, HMO and MNDO molecular orbitals and the HMO approach on pericyclic reactions presented by Tang.     

Electrostatic interactions between substituents as regioselectivity control elements in Diels-Alder cycloadditions. A DFT study of cycloadditions of 1-methoxy-4-trimethylsiloxy dienes with acrylonitrile

The regioselectivities of Diels-Alder reactions of 1-methoxy-4-trimethylsiloxy-1,3-butadiene and the corresponding o-xylylene with acrylonitrile were explored with density functional theory. The transition state of the reaction of the diene with acrylonitrile was studied in both the gas phase and in a low dielectric (epsilon = 2.247) solvent. The regioselectivities of these reactions are predicted to be controlled by the direct electrostatic interactions between the diene and dienophile substituents. The electron-donating capacities of methoxy and trimethylsiloxy substituents are shown to be very similar and to not contribute to regioselectivity control. A prediction is made that the cycloadditions of the o-xylylene will be unselective, while 1-methoxy-4-trimethylsiloxy-1,3-butadiene will give a small preference ( approximately 5:1) in favor of the proximal methoxy and cyano groups. The thermochromic behavior of trans-disubstituted disiloxy benzocyclobutene was also explored.     

Shape groups of the electronic isodensity surfaces for small molecules: Shapes of 10-electron hydrides

An algorithm for a detailed 3-D characterization of the shapes of molecular charge distributions is implemented in the form of a comprehensive package of computer programs, GSHAPE, and applied to a series of 10-electron hydrides to critically evaluate the methodology. Attention is paid to the effects of nuclear geometry and the size of basis on the molecular shape. The characterization is performed by computing a number of topological invariants (“shape groups”) associated with a continuum of molecular surfaces: the complete family of all electronic isodensity contours for the given molecules. These shape groups (the homology groups of truncated surfaces derived from isodensity contours) depend on two continuous parameters: a density value defining the density contour and a reference curvature value, to which the local curvatures of the isodensity contours are compared. The electronic charge distribution is calculated at the ab initio level using basis sets ranging from STO-3G to 6-31G**. No visual inspection is required for the characterization and comparison of shapes of molecular charge densities, as these are done algorithmically by the computer. However, visualization of the results is one option of our program using Application Visualization Software (AVS). For a given molecule, in a given nuclear geometry, the technique provides a 2-D shape map, displaying the distribution of the shape gruops as a function of the local curvature and the level set value (the value of the charge density at the contour). The computer program GSHAPE performs the analysis automatically. This feature makes it potentially useful in the context of computer-aided drug design, where unbiased, automated shape characterization methods are valuable tools. As examples, a variety of 2-D shape maps are discussed. © John Wiley & Sons, Inc.     

Theoretical evaluation of the origin of the regio- and stereoselectivity in the Diels-Alder reactions of dialkylvinylboranes: studies on the reactions of vinylborane, dimethylvinylborane, and vinyl-9-BBN with trans-piperylene and isoprene

Ab initio and DFT calculations have been performed to study the origin of the regio- and stereoselectivity of the Diels-Alder reactions of dialkylvinylboranes with substituted dienes. B3LYP/6-31G energies of the transition structures for the reactions of dimethylvinylborane and vinyl-9-BBN with trans-piperylene and isoprene yielded calculated ratios which are in very good agreement with experimental values. Nonclassical carbon-boron [4+3] secondary orbital interactions seem to account for the high endo stereoselectivity of these reactions. However, C-B interactions become less important when the bulkiness of the alkyl groups attached to boron increases. Both endo and exo transition structures for the reactions of dimethylvinylborane and vinyl-9-BBN adopt classical [4+2] character. This study also extends Singleton's investigation on butadiene to regioselectivity. FMO theory has been used to rationalize the lack of regioselectivity in the reactions of dimethylvinylborane. The anomalous meta regioselectivity of the Diels-Alder reaction of vinyl-9-BBN with trans-piperylene is mainly caused by steric effects.     

3-亚甲基苯并吡喃-2,4-二酮与烯醇硅醚的Diels-Alder反应合成3,4- 二氢-2H,5H-吡喃并[3,2-c][1]苯并吡喃-5-酮衍生物

通过4-羟基香豆素与苯甲醛、甲醛和戊醛缩合产生的quinone methide与烯醇硅醚的Diels-Alder反应, 以较高产率合成了一系列含有硅氧基的3,4-二氢-2H,5H-吡喃并[3,2-c][1]苯并吡喃-5-酮衍生物. 用X射线单晶衍射确定了其中5个化合物的空间构型. 利用密度泛函(DFT)方法计算反应物之间的前线分子轨道相互作用, 对反应的区域选择性进行了研究, 计算结果与实验值相符.     

硅杂苯与亲二烯体的Diels-Alder反应

采用密度泛函理论(DFT)在B3LYP/6-311G(d,p)水平上研究了硅杂苯与一些亲二烯体的两类可能的Diels-Alder反应的微观机理、势能剖面、取代基效应和溶剂化效应. 计算结果表明, 所研究反应均以协同的方式进行. 亲二烯体分子碳原子上的苯基取代基对两个新键形成的非同步性和反应的活化能垒的影响取决于苯基在产物中的相对位置, 而硅杂苯分子中硅原子上的CCl3取代基有利于杂Diels-Alder反应的进行. 形成一个C—Si键的杂Diels-Alder反应在热力学和动力学上均远比相应的全碳Diels-Alder反应容易进行, 实验观察到的杂Diels-Alder反应中的区域选择性由动力学因素所控制. 硅杂苯与烯烃的反应比与相应炔烃的反应在动力学上容易进行一些, 但在热力学上后者远比前者容易进行. 苯溶剂对所研究反应的势能剖面影响较小.     

Characterization of the switch in the mechanism of an intramolecular Diels-Alder reaction

Changing the dienophile moiety of an intramolecular Diels-Alder (IMDA) cycloaddition from an allyl ether to an allenyl ether can dramatically change the regioselectivity. We hereby show by density functional theory computations that such unprecedented divergence is produced by an underlying change in the mechanism of the reaction. The allyl ether yields a fused tetrahydrofuran through a classical Diels-Alder reaction, whereas the allenyl ether yields a (methylidene)tetrahydropyran through a stepwise process. The latter reaction involves an extreme asynchronism in the bond-forming events with a diradicaloid intermediate that is stabilized by conjugation and synergistic (captodative) effects. Comparison with intermolecular model D-A reactions, which are concerted processes with various degrees of asynchrony, helps explain the change in regioselectivity for the IMDA reaction of allyl systems and the shift in mechanism for the IMDA reaction of the allenyl derivatives studied.     

Transition states and mechanisms of the hetero-Diels-Alder reactions of hyponitrous acid, nitrosoalkanes, nitrosoarenes, and nitrosocarbonyl compounds.

The transition states and energetics of Diels-Alder reactions for a variety of nitroso compounds with dienes were explored with density functional theory using the B3LYP functional and 6-31G basis set. The reactions involve HNO, various nitrosoalkanes and arenes (RNO and ArNO), and nitrosoformaldehyde (CHONO) as dienophiles with butadiene and a series of 1- and 2-substituted dienes. The mechanisms, activation energies, energies of reaction, stereoselectivities, and regioselectivities are predicted for these reactions. These predictions are compared to available experimental data. The mechanism is found to be concerted but involves highly asynchronous transition states. Although it is not evident in the products, we find that the endo path is very strongly favored over the exo alternative due to repulsion between the diene and nitrogen's lone pair. A range of experimental regioselectivities are reproduced by calculations and are found to hinge on a very sensitive balance between FMO interactions, electrostatics, and steric effects. A series of generalizations for predicting regioselectivity for untried diene-dienophile pairs are made.     

Interactions of molecules with nucleic acids. IX. Evaluation and presentation of electrostatic contours on a steric surface with the removal of hidden lines

A technique to generate electrostatic contours on a steric surface is presented and applied to the presentation of molecules that interact with DNA. A set of electrostatic points at predetermined values along with their derivatives are obtained on the steric contours as they are generated. The steric contours are generated in a set of parallel planes. Points with given electrostatic values are then connected between and within the contours mathematically with a Taylor's expansion and two rules: the first to tentatively line up points that can be connected, and the second to check to insure that the remaining points can be connected. This method insures that contours will not cross by requiring that a possible connection of two points leaves an even number of remaining points for each electrostatic value in isolated regions of unused points bounded by points that have already been connected. The hidden line algorithm used previously to draw molecules in a space-filling model within the context of steric contours is applied to the complete problem of the presentation of a molecule bound to DNA with steric contours in parallel planes, and with electrostatic contours drawn on this steric surface.     

Regiochemical control in the diels-alder reactions of substituted naphthoquinones: orientation in the synthesis of benz[a]anthraquinones

The regioselectivity in the Diels-Alder reactions of styrene with certain substituted 1,4-naphthoquinones was explored. The results were consistent with predictions based upon analysis of dione polarization.     

锗苯与亲二烯体的Diels-Alder反应的理论研究

采用密度泛函理论方法在B3LYP/6-311G(d,p)水平上研究了锗苯与一些亲二烯体的Diels-Alder反应的微观机理和势能剖面, 考察了取代基和苯溶剂对反应势能剖面的影响, 探讨了杂Diels-Alder反应中区域选择性的起源. 计算结果表明, 所研究反应均以协同的方式进行. 亲二烯体分子碳原子上的苯基取代基对杂Diels-Alder反应中2个新键形成的非同步性和活化能垒的影响与最终产物中苯基和锗原子间的相对位置有关, 锗苯分子中锗原子上的CCl3取代基在热力学和动力学上均有利于反应的进行. 苯溶剂对所研究反应的势能剖面影响较小. 实验观察到的杂Diels-Alder反应的区域选择性由动力学因素所控制.     

Regiochemistry of the Diels-Alder Reaction of 1-Ethenyl-hydronaphthalenes and 2-Methyl-2-cyclopenten-1-one

Diels-Alder reactions of 2-methyl-2-cyclopenten-l-one with l-ethenylhydronaphthalenes are described. The structure analysis of the reaction products by NMR spectroscopy is reported. The regioselectivity as well as the diastereoselectivity of the cycloadditions are discussed.     

Representation of molecular electrostatic potentials of biopolymer by self‐organizing feature map

The Kohonen self‐organizing map was introduced to map the protein molecular surface features. The protein or polypeptide properties, such as shape and molecular electrostatic potential, can be visualized by self‐organizing map, which was trained by the 3D surface coordinates. Such maps allow the visual comparison of molecular properties between proteins having common topological or chemical features.     

Highly regioselective Diels-Alder reactions toward oroidin alkaloids: use of a tosylvinyl moiety as a nitrogen masking group with adjustable electronics

[reaction: see text] The use of the p-toluenesulfonyl (Ts) and tosylvinyl (Tsv) groups as nitrogen masking groups imparted high regioselectivity in Diels-Alder reactions directed toward members of the oroidin-derived marine alkaloid family. The electron-withdrawing Tsv group was utilized as an electronically adjustable nitrogen-protecting group as subsequent hydrogenation provided the more electron-rich tosylethyl (Tse) group. This electronic adjustment strategy avoided a protecting group exchange and provided the required electronics for the key chlorination/ring-contraction sequence.     

Steering On‐Surface Reactions by a Self‐Assembly Approach

4,4′‐Bis(2,6‐difluoropyridin‐4‐yl)‐1,1′:4′,1′′‐terphenyl (BDFPTP) molecules underwent dehydrocyclization and covalent coupling reactions on Au(111) according to scanning tunneling microscopy (STM) measurements and density functional theory (DFT) calculations. Self‐assembly of the reactants in well‐defined molecular domains prior to reaction could greatly enhance the regioselectivity of the dehydrocyclization reaction and suppress defluorinated coupling, demonstrating that self‐assembly can efficiently steer on‐surface reactions. Such a strategy could be of great importance in surface chemistry and widely applied to control on‐surface reactions.     

A study of solvent effects on the stereoselectivity of Diels-Alder reactions through molecular surface electrostatic potentials

Statistical models for the study of solvent effects on the endo/exo selectivity of Diels-Alder reactions using molecular surface electrostatic potentials was obtained. The models show that hydrogen bond interactions of solvent molecules favor the predominance of the endo isomer for the reaction of methyl acrylate, methyl methacrylate and methyl trans-crotonate with cyclopentadiene whereas the effect of solvophobicity seems to be negligible.