The effect of numerical error on the reproducibility of molecular geometry optimizations

Geometry optimization is one of the most often applied techniques in computational drug discovery. Although geometry optimization routines are generally deterministic, the minimization trajectories can be extremely sensitive to initial conditions, especially in case of larger systems such as proteins. Simple manipulations such as coordinate transformations (translations and rotations), file saving and retrieving, and hydrogen addition can introduce small variations ( approximately 0.001 A) in the starting coordinates which can drastically affect the minimization trajectory. With large systems, optimized geometry differences of up to 1 A RMSD and final energy differences of several kcal/mol can be observed when using many commercially available software packages. Differences in computer platforms can also lead to differences in minimization trajectories. Here we demonstrate how routine structure manipulations can introduce small variations in atomic coordinates, which upon geometry optimization, can give rise to unexpectedly large differences in optimized geometries and final energies. We also show how the same minimizations run on different computer platforms can also lead to different results. The implications of these findings on routine computational chemistry procedures are discussed.     

Theoretical study of catalytic efficiency of a Diels-Alderase catalytic antibody: an indirect effect produced during the maturation process

The Diels-Alder reaction is one of the most important and versatile transformations available to organic chemists for the construction of complex natural products, therapeutics agents, and synthetic materials. Given the lack of efficient enzymes capable of catalyzing this kind of reaction, it is of interest to ask whether a biological catalyst could be designed from an antibody-combining site. In the present work, a theoretical study of the different behavior of a germline catalytic antibody (CA) and its matured form, 39 A-11, that catalyze a Diels-Alder reaction has been carried out. A free-energy perturbation technique based on a hybrid quantum-mechanics/molecular-mechanics scheme, together with internal energy minimizations, has allowed free-energy profiles to be obtained for both CAs. The profiles show a smaller barrier for the matured form, which is in agreement with the experimental observation. Free-energy profiles were obtained with this methodology, thereby avoiding the much more demanding two-dimensional calculations of the energy surfaces that are normally required to study this kind of reaction. Structural analysis and energy evaluations of substrate-protein interactions have been performed from averaged structures, which allows understanding of how the single mutations carried out during the maturation process can be responsible for the observed fourfold enhancement of the catalytic rate constant. The conclusion is that the mutation effect in this studied germline CA produces a complex indirect effect through coupled movements of the backbone of the protein and the substrate.     

催化光度法时间程序测定土壤中痕量碘

碘是评价环境的重要元素之一,是地球化学勘察样品常测元素。本实验建立了艾斯卡试剂分解-热水提取样品,催化分光光度法时间程序测定碘的方法。详细讨论了艾斯卡试剂手工制作与行星球磨机制作的利弊;;参比液的选择;17℃-25℃不同环境温度条件对实验结果的影响;全程序空白溶液,与36g/L的碳酸钠溶液两种方法制作标准曲线及标准曲线线性范围;样品烧结时间及温度;乙酸用量对样品测试吸光度的影响。结果表明：利用行星球磨机制作艾斯卡试剂,选择试剂空白为参比液,在19℃的恒温环境下,采用36g/L的碳酸钠溶液制作0-8ug/mL标准曲线,样品采用0-300℃、300-500℃、500-750℃三阶段升温,750℃保持30min的烧结程序,乙酸用量为5mL时可以得到可靠的结果。该方法克服了艾斯卡试剂制作困难、样品烧结结块及实验反应速率过快等困难。通过方法学考察表明：基于所建方法碘元素校准曲线系数＞0.999;方法检出限为0.2 mg/kg;测定GSS36、GSS37、GSS38、GSS40、GSS47、GSS48、GSS49等9种国家一级标准物质,结果均在参考值范围内,相对标准偏差RSD＜5%。该方法测定的结果准确度及精密度高、 检出限低、减少碘记忆效应的存在,适用于地球化学勘察土壤样品中碘的测定。     

超级微波消解-电感耦合等离子体发射光谱（ICP-OES）法测定土壤中18种元素

为提高土壤多元素同时检测的效率,采用超级微波消解-电感耦合等离子体发射光谱法测定土壤中钾、钠、钙、镁、铜、铁、锰、锌、磷、硫、硼、砷、镉、铬、铅、钴、镓、锂等18种元素含量。比较了超级微波消解、常规微波消解和电热板消解的处理效果,采用超级微波消解法对样品进行前处理,并优化了消解条件。在最优条件下,各元素的检出限在0.05~20 mg/kg,加标回收率在86.2%~107.5%,RSD在0.1%~3.0%,方法准确度及精密度可以满足多元素同时测定的需求,且该方法具有简单、快速、成本低、用酸量少、重现性好等特点。     

电感耦合等离子体质谱(ICP-MS)法测定土壤中的碘

通过电感耦合等离子体质谱法(ICP-MS)测定土壤中的碘。样品预处理采用艾斯卡试剂熔融、热水提取和阳离子树脂静态交换,试验加入了不同剂量的阳离子交换树脂在不同程度上降低了溶液中Na+ 和Zn2+^{等阳离子的盐效应干扰。研究了乙醇在}ICP-MS中对碘元素的增强效应,用3%的氨水溶液清洗进样系统,有效减少的碘的记忆效应和清洗时间。该方法线性范围宽,方法灵敏度高,检出限低,试剂用量少,环境友好。对苏州及周边区域若干非污染土壤点位进行采样、制备和测试,碘平均含量为2.7μg.g_-1^;同步测试国家有证标准物质,精密度和准确度良好。     

Quantification of Stereochemical Communication in Metal–Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal–organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per “incorrect” amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra‐ and inter‐vertex coupling constants are used to track the degree of stereochemical communication across a range of metal–organic assemblies (employing different ligands, peripheral amines, and metals); temperature‐dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal–organic container molecules.     

Reference spectra of important adsorbed organic and inorganic phosphate binding forms for soil P speciation using synchrotron‐based K‐edge XANES spectroscopy

Direct speciation of soil phosphorus (P) by linear combination fitting (LCF) of P K‐edge XANES spectra requires a standard set of spectra representing all major P species supposed to be present in the investigated soil. Here, available spectra of free‐ and cation‐bound inositol hexakisphosphate (IHP), representing organic P, and of Fe, Al and Ca phosphate minerals are supplemented with spectra of adsorbed P binding forms. First, various soil constituents assumed to be potentially relevant for P sorption were compared with respect to their retention efficiency for orthophosphate and IHP at P levels typical for soils. Then, P K‐edge XANES spectra for orthophosphate and IHP retained by the most relevant constituents were acquired. The spectra were compared with each other as well as with spectra of Ca, Al or Fe orthophosphate and IHP precipitates. Orthophosphate and IHP were retained particularly efficiently by ferrihydrite, boehmite, Al‐saturated montmorillonite and Al‐saturated soil organic matter (SOM), but far less efficiently by hematite, Ca‐saturated montmorillonite and Ca‐saturated SOM. P retention by dolomite was negligible. Calcite retained a large portion of the applied IHP, but no orthophosphate. The respective P K‐edge XANES spectra of orthophosphate and IHP adsorbed to ferrihydrite, boehmite, Al‐saturated montmorillonite and Al‐saturated SOM differ from each other. They also are different from the spectra of amorphous FePO₄, amorphous or crystalline AlPO₄, Ca phosphates and free IHP. Inclusion of reference spectra of orthophosphate as well as IHP adsorbed to P‐retaining soil minerals in addition to spectra of free or cation‐bound IHP, AlPO₄, FePO₄ and Ca phosphate minerals in linear combination fitting exercises results in improved fit quality and a more realistic soil P speciation. A standard set of P K‐edge XANES spectra of the most relevant adsorbed P binding forms in soils is presented.     

Uncertainty principles associated with quaternionic linear canonical transforms

In the present paper, we generalize the linear canonical transform (LCT) to quaternion‐valued signals, known as the quaternionic LCT (QLCT). Using the properties of the LCT, we establish an uncertainty principle for the two‐sided QLCT. This uncertainty principle prescribes a lower bound on the product of the effective widths of quaternion‐valued signals in the spatial and frequency domains. It is shown that only a Gaussian quaternionic signal minimizes the uncertainty. Copyright © 2016 John Wiley & Sons, Ltd.