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CoMFA, CoMSIA and GRID/GOLPE studies on calcium entry blocking 1,4-dihydropyridines CoMFA, CoMSIA和GRID/GOLPE研究钙进入阻断1,4-二氢吡啶
Pub Date : 2002-08-01 DOI: 10.1002/1521-3838(200208)21:3<239::AID-QSAR239>3.0.CO;2-W
K. Schleifer, E. Tot
Three different 3D QSAR methods have been applied for a common pharmacophore model of 45 calcium antagonistically active 1,4-dihydropyridines (DHP) in order to find best correlation of interaction fields and biological activity. Analysis for the entire data set yielded r2/q values in a range starting from 0.821/0.620 (GRID/GOLPE) over 0.872/0.600 (CoMFA) to 0.908/0.744 (CoMSIA). The robustness of these models was tested not only via leave-one-out but also by leave-9-out crossvalidations. Furthermore, models were constructed using a subset of 37 DHPs (training set) allowing the prediction of activity for the residual 8 DHPs (test set). The training set yielded r2/q values starting from 0.826/0.672 (GRID/GOLPE) over 0.872/0.540 (CoMFA) to 0.899/0.662 (CoMSIA). For the test set r values from 0.677 (GRID/GOLPE) over 0.639 (CoMFA) to 0.470 (CoMSIA) were calculated. Besides the statistics, each 3D QSAR model yields further information by analysis of the generated contour maps. Consideration of the CoMFA and CoMSIA fields indicates unfavourable steric interactions for bulky moieties in 4′-position. On the other hand, sterical demanding 2′- and 3′-substituents are favourable and the biological activity of DHPs is further increased if these moieties produce a negative electrostatic potential. In contrast, high π-electron density on top of and parallel to the 4-phenyl ring beside the 2′-position is associated with decreasing activity. This could point to repulsive electronic interactions with binding site residues or to the potential of electron-deficient 4-aryl moieties to behave as electron acceptors in a charge transfer (CT) mechanism.
采用三种不同的三维QSAR方法对45种具有钙拮抗活性的1,4-二氢吡啶(DHP)的药效团模型进行了研究,以寻找相互作用场与生物活性的最佳相关性。对整个数据集的分析得出r2/q值的范围从0.821/0.620 (GRID/GOLPE)超过0.872/0.600 (CoMFA)到0.908/0.744 (CoMSIA)。这些模型的稳健性不仅通过留一和留九的交叉验证来检验。此外,使用37个dhp(训练集)的子集构建模型,允许预测剩余8个dhp(测试集)的活动。训练集产生的r2/q值从0.826/0.672 (GRID/GOLPE)超过0.872/0.540 (CoMFA)到0.899/0.662 (CoMSIA)。对于测试集,r值从0.677 (GRID/GOLPE) / 0.639 (CoMFA)到0.470 (CoMSIA)计算。除了统计数据外,每个3D QSAR模型还可以通过分析生成的等高线地图来获得进一步的信息。CoMFA场和CoMSIA场的研究表明,在4 '位置上的大块分子的空间相互作用是不利的。另一方面,2 ' -和3 ' -取代基是有利的,如果这些部分产生负静电电位,则DHPs的生物活性进一步增加。相反,在4-苯基环的2′位置附近,其上方和平行的π电子密度越高,活性越低。这可能指向与结合位点残基的排斥性电子相互作用或缺乏电子的4-芳基部分在电荷转移(CT)机制中充当电子受体的潜力。
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引用次数: 11
Application of Density Functional Theory Based Car-Parrinello Simulations to the Study of Catalytic Processes 基于密度泛函理论的Car-Parrinello模拟在催化过程研究中的应用
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<149::AID-QSAR149>3.0.CO;2-#
S. Raugei, Dongsup Kim, M. Klein
We review recent applications of density functional theory based Car-Parrinello molecular dynamics simulations to the study of the structure and reactivity of liquid superacids. We first discuss the nature of an excess proton in liquid hydrofluoric acid, which can be considered as the simplest model of a liquid superacid. Then, we analyze the origin of the superacidity of real superacids in two limiting cases, namely in boron triflouride and antimony pentafluoride in hydrofluoric acid solutions, which are one of the weakest and the strongest known superacids, respectively. We conclude by discussing some aspects of the chemical reactivity of carbon monoxide and simple hydrocarbons in SbF5/HF solutions.
本文综述了基于密度泛函理论的Car-Parrinello分子动力学模拟在液体超强酸结构和反应性研究中的最新应用。我们首先讨论了液体氢氟酸中多余质子的性质,它可以被认为是液体超强酸的最简单模型。然后,我们分析了两种极限情况下,即三氟化硼和五氟化锑在氢氟酸溶液中的超强酸的来源,这两种情况分别是已知最弱和最强的超强酸之一。最后,我们讨论了一氧化碳和简单碳氢化合物在SbF5/HF溶液中的化学反应性。
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引用次数: 2
Exploring Organic Chemistry with DFT: Radical, Organo‐metallic, and Bio‐organic Applications 用DFT探索有机化学:自由基、有机金属和生物有机的应用
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<128::AID-QSAR128>3.0.CO;2-B
F. Bernardi, A. Bottoni, M. Garavelli
In this review we report the results of DFT investigations which have been carried out in different fields of organic and organometallic chemistry, including radical reactivity, structure and reactivity of organometallic compounds, and biochemical/biophysical properties of long chain unsaturated systems. Many of the most popular non-local corrected functionals (e.g. B3LYP, BHLYP, BLYP, BP86) have been benchmarked both versus experimental and high level ab initio (e.g. MP2, MP4, CAS-SCF/CAS-PT2) data, resulting in an impressive agreement. The DFT approach appears to be a powerful tool, which can be used as a valid alternative to more traditional correlated methods, to achieve mechanistic information of chemical/ physical interest in the modelling of organic and biochemical systems. In particular, in the examples selected in this review, we discuss the results obtained for the addition reaction of alkyl radicals to double bonds and for the hydrogen/ chlorine abstraction reaction by alkyl and silyl radicals from various organic substrates. Moreover, binding interactions (i.e. geometries and energies) in organometallic compounds are shown to be satisfactorily reproduced via DFT and examples of nickel-catalyzed [2 + 2] cycloaddition reaction and homogeneous Ziegler-Natta catalysis are investigated. Finally, a DFT modelling for the singlet-oxygen quenching ability and radical trapping activity of carotenes is presented. The simulated data provide a rationale for the protective action of carotenes observed in biological tissues and elucidates the physical and chemical mechanisms involved in the reactivity of carotenes versus oxygen and radicals.
本文综述了DFT在有机化学和金属有机化学不同领域的研究成果,包括自由基反应性、金属有机化合物的结构和反应性以及长链不饱和体系的生化/生物物理性质。许多最流行的非局部校正函数(如B3LYP、BHLYP、BLYP、BP86)已经与实验和高水平从头计算(如MP2、MP4、CAS-SCF/CAS-PT2)数据进行了基准测试,结果令人印象深刻。DFT方法似乎是一个强大的工具,它可以作为更传统的相关方法的有效替代,在有机和生化系统的建模中获得化学/物理感兴趣的机械信息。特别地,在本文所选的例子中,我们讨论了烷基自由基与双键加成反应的结果,以及烷基和硅基自由基从各种有机底物中提取氢/氯反应的结果。此外,有机金属化合物中的结合相互作用(即几何形状和能量)通过DFT得到了令人满意的再现,并研究了镍催化的[2 + 2]环加成反应和均相齐格勒-纳塔催化的例子。最后,提出了胡萝卜素单线态氧猝灭能力和自由基捕获活性的DFT模型。模拟数据为在生物组织中观察到的胡萝卜素的保护作用提供了理论依据,并阐明了胡萝卜素对氧和自由基反应性的物理和化学机制。
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引用次数: 21
Applications of density functional theory-based methods in medicinal chemistry 基于密度泛函理论的方法在药物化学中的应用
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<173::AID-QSAR173>3.0.CO;2-B
M. Sulpizi, G. Folkers, U. Rothlisberger, P. Carloni, L. Scapozza
With the advances in genomics, proteomics and functional genomics new therapeutic targets to be tackled by medicinal chemistry are expected. This article reviews applications of first principle methods to address medicinal chemistry issue related to drug/target interactions. Two selected representative case studies involving therapeutically interesting targets are presented. The first case study presents how DFT can contribute to ameliorate scoring functions for drug screening in particular by enabling the discrimination between inhibitors and substrates. The second example shows the use of DFT within the framework of a QM/MM mixed approach for elucidating mechanisms of reaction. This approach allows defining the electronic state and structure of the reaction transition state whose knowledge is essential for designing potent and specific transition state analogs inhibitors. Finally, addressing the issue of other medicinal chemistry related application of DFT we suggest that DFT has indeed the potentiality of becoming very important for challenging new issues presented to medicinal chemistry in the post genomic era.
随着基因组学、蛋白质组学和功能基因组学的发展,药物化学有望攻克新的治疗靶点。本文综述了第一性原理方法在解决药物/靶标相互作用相关的药物化学问题中的应用。两个选定的代表性案例研究涉及治疗有趣的目标提出。第一个案例研究介绍了DFT如何有助于改善药物筛选的评分功能,特别是通过区分抑制剂和底物。第二个例子显示了在QM/MM混合方法的框架内使用DFT来阐明反应机制。这种方法允许定义反应过渡态的电子态和结构,其知识对于设计有效和特定的过渡态类似物抑制剂至关重要。最后,针对其他与DFT相关的药物化学应用问题,我们认为DFT确实有潜力在后基因组时代对药物化学提出的新问题提出挑战。
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引用次数: 35
Introduction to density-functional theory and ab-initio molecular dynamics 密度泛函理论及从头算分子动力学导论
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<97::AID-QSAR97>3.0.CO;2-6
R. Car
Density-Functional-Theory (DFT) provides a general framework to deal with the ground-state energy of the electrons in many-atom systems. Its history dates back to the work of Thomas [1], Fermi [2] and Dirac [3] who devised approximate expressions for the kinetic energy [1, 2] and the exchange energy [3] of many-electron systems in terms of simple functionals of the local electron density. These ideas were further elaborated in the Xα method of Slater [4], until finally, the foundations of the modern theory were laid down in the mid-sixties by Kohn and collaborators [5, 6]. Since then but particularly in the last two decades the number of applications of DFT to electronic structure problems has grown dramatically. Today DFT is the method of choice for first-principles electronic structure calculations in condensed phase and complex molecular environments. DFT based approaches are used in a variety of disciplines ranging from condensed matter physics, to chemistry, materials science, biochemistry and biophysics. There are several reason for this success: (i) DFT makes the many-body electronic problem tractable at a numerical cost of self-consistent-field single particle calculations; (ii) despite the severe approximations made to the exchange and correlation energy functional, DFT calculations are usually sufficiently accurate to predict materials structures or chemical reactions products; (iii) currently available computational power and modern numerical algorithms make DFT calculations feasible for realistic models of systems like e.g. an interface between two crystalline materials, a carbon nanotube, or the active site of an enzyme.
密度泛函理论(DFT)提供了一个处理多原子系统中电子基态能量的一般框架。它的历史可以追溯到托马斯[1],费米[2]和狄拉克[3]的工作,他们用局部电子密度的简单泛函设计了多电子系统的动能[1,2]和交换能[3]的近似表达式。这些想法在斯莱特的Xα方法中得到了进一步的阐述[4],直到最后,现代理论的基础在60年代中期由Kohn和合作者奠定[5,6]。从那时起,特别是在过去的二十年中,DFT在电子结构问题上的应用数量急剧增长。目前,DFT是凝聚态和复杂分子环境中第一性原理电子结构计算的首选方法。基于DFT的方法被用于从凝聚态物理到化学、材料科学、生物化学和生物物理学的各种学科。这一成功有几个原因:(i) DFT使多体电子问题变得易于处理,而代价是自洽场单粒子计算的数值代价;(ii)尽管对交换和相关能泛函进行了严格的近似,但DFT计算通常足以准确地预测材料结构或化学反应产物;(iii)目前可用的计算能力和现代数值算法使DFT计算在系统的实际模型中可行,例如两种晶体材料之间的界面,碳纳米管或酶的活性位点。
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引用次数: 46
Density Functional Theory‐Based Molecular Dynamics of Biological Systems 基于密度泛函理论的生物系统分子动力学
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<166::AID-QSAR166>3.0.CO;2-3
P. Carloni
Density functional theory based molecular dynamics (DFT-MD), play an increasingly important role for the modeling of biological systems. Here we outline the principles of the DFT-MD method. Subsequently, we present selected applications in nucleic acid and enzyme chemistry, which are meant to illustrate the power and current limitations of the DFT-MD method for biomolecular simulation.
基于密度泛函理论的分子动力学(DFT-MD)在生物系统建模中发挥着越来越重要的作用。这里我们概述了DFT-MD方法的原理。随后,我们介绍了在核酸和酶化学中的应用,这意味着说明DFT-MD方法用于生物分子模拟的能力和当前的局限性。
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引用次数: 8
Computation of spectroscopic parameters in vacuo and in condensed phases by methods based on the density functional theory 用密度泛函理论计算真空和凝聚相的光谱参数
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<105::AID-QSAR105>3.0.CO;2-V
V. Barone, O. Crescenzi, R. Improta
The impact of density functional theory in the computation of reliable spectroscopic parameters is reviewed with special reference to IR, Raman, UV, visible, NMR and EPR techniques. In general terms, the results delivered by the most recent density functionals (especially hybrid ones) are remarkably accurate. Proper treatment of solvent effects by continuum models and of vibrational averaging effects by suitable Hamiltonians governing the nuclear motions, significantly increases the reliability of the results and the fields of application of theoretical computations. Some case examples have been reported to better illustrate the potentialities of this approach also for non specialists.
本文综述了密度泛函理论在可靠光谱参数计算中的影响,特别是红外、拉曼、紫外、可见、核磁共振和EPR技术。一般来说,最近的密度泛函(特别是混合泛函)给出的结果非常准确。用连续介质模型正确地处理溶剂效应,用适当的哈密顿量来处理核运动的振动平均效应,大大增加了结果的可靠性和理论计算的应用范围。已经报道了一些案例,以更好地说明这种方法也适用于非专业人员的潜力。
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引用次数: 17
Hybrid Car-Parrinello/molecular mechanics modelling of transition metal complexes: Structure, dynamics and reactivity 混合动力Car-Parrinello/过渡金属配合物的分子力学建模:结构、动力学和反应性
Pub Date : 2002-07-01 DOI: 10.1002/1521-3838(200207)21:2<119::AID-QSAR119>3.0.CO;2-B
L. Guidoni, P. Maurer, S. Piana, U. Rothlisberger
The theoretical modelling of chemically active transition metal (TM) centres is a notoriously difficult task. The metal-ligand interactions in these complexes are often highly directional and the concoction of suitable analytic interaction potentials can be far from trivial. The situation is rendered even more difficult by the fact that at finite temperature, the system might switch dynamically between different bonding situations or exhibit several energetically close-lying spin states which are all characterized by different coordination numbers and geometries. In this article, we describe the structural, dynamical and reactive properties of complex TM-containing systems with the help of a mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics approach, in which the TM centre is described with generalized gradient corrected density functional theory embedded in a classical force field description. The power of such a combined Car-Parrinello/molecular mechanics approach is illustrated with a number of representative examples ranging from enantioselective TM catalysts to radiopharmaceuticals and metalloenzymes.
化学活性过渡金属(TM)中心的理论建模是一项非常困难的任务。这些配合物中的金属-配体相互作用通常具有高度的方向性,而适当的分析相互作用势的混合可能远非微不足道。在有限温度下,系统可能在不同的键合状态之间动态切换,或表现出几个能量紧密的自旋态,这些自旋态都具有不同的配位数和几何形状,这使得情况变得更加困难。在本文中,我们借助混合量子力学/分子力学(QM/MM)分子动力学方法描述了含TM的复杂系统的结构、动力学和反应性质,其中TM中心用嵌入在经典力场描述中的广义梯度校正密度泛函理论来描述。从对映选择性TM催化剂到放射性药物和金属酶,许多具有代表性的例子说明了这种Car-Parrinello/分子力学结合方法的力量。
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引用次数: 11
NMR Study of Conformational Preferences of Inhibitors of Monoamine Uptake 单胺摄取抑制剂构象偏好的核磁共振研究
Pub Date : 2002-05-01 DOI: 10.1002/1521-3838(200205)21:1<38::AID-QSAR38>3.0.CO;2-J
M. Appell, Aleksej Krunic, Tony Jeen Choi, S. Mariappan, W. Dunn, M. Reith
We have used the recently developed tensor decomposition 3D-QSAR method to predict the conformation and alignment of cocaine derivatives bound to the monoamine transporters, NET, DAT and SERT. The analysis revealed that the ligands bind to the receptors in a conformation with the 3β-aryl group orthogonal or approximately orthogonal to the tropane ring. Semi rigid ligands have been prepared with a 3β-aryl group having strong conformational preferences for this orientation. Two compounds had affinities for the DAT and SERT in the low nanomolar range. The solution conformation of one compound has been determined and the results support the results of the 3D-QSAR analysis. Comparisons of affinities and selectivities of these ligands are discussed.
我们使用最近开发的张量分解3D-QSAR方法来预测与单胺转运蛋白NET、DAT和SERT结合的可卡因衍生物的构象和排列。分析表明,配体与受体的结合呈3β-芳基与tropane环正交或近似正交的构象。半刚性配体是用对该取向具有强烈构象偏好的3β-芳基制备的。两种化合物在低纳摩尔范围内对DAT和SERT具有亲和性。测定了其中一种化合物的溶液构象,结果支持了3D-QSAR分析的结果。讨论了这些配体的亲和性和选择性的比较。
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引用次数: 0
Fragmental Methods in the Design of New Compounds. Applications of The Advanced Algorithm Builder 新化合物设计中的片段化方法。高级算法生成器的应用
Pub Date : 2002-05-01 DOI: 10.1002/1521-3838(200205)21:1<23::AID-QSAR23>3.0.CO;2-E
P. Japertas, R. Didziapetris, A. Petrauskas
Fragmental methods (FMs) have great potential in many practical areas related to the design of new lead compounds. Advanced Algorithm BuilderTM (AAB) is a new software system which employs FMs in (i) building QSPR, QSAR and SAR models, (ii) converting them to custom (in-house) algorithms and screening filters, and (iii) predicting physical properties and biological activities for new compounds. This review demonstrates how FMs and AAB can be used to substantiate our intuition, interpret observations, validate hypotheses and obtain new algorithms for predicting physical properties and biological activities. Applications for practical and theoretical chemists in the design of new lead compounds are discussed.
碎片化方法在许多与新先导化合物设计相关的实际领域具有巨大的潜力。Advanced Algorithm BuilderTM (AAB)是一个新的软件系统,它使用FMs来(i)构建QSPR, QSAR和SAR模型,(ii)将它们转换为定制(内部)算法和筛选过滤器,以及(iii)预测新化合物的物理性质和生物活性。这篇综述展示了FMs和AAB如何用于证实我们的直觉,解释观察结果,验证假设,并获得预测物理性质和生物活性的新算法。讨论了实际化学家和理论化学家在新先导化合物设计中的应用。
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引用次数: 60
期刊
Quantitative Structure-activity Relationships
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