Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

3-D vertical ray shooting and 2-D point enclosure, range searching, and arc shooting amidst convex fat objects

We present a new data structure for a set of n convex simply-shaped fat objects in the plane, and use it to obtain efficient and rather simple solutions to several problems including (i) vertical ray shooting—preprocess a set of n non-intersecting convex simply-shaped flat objects in 3-space, whose xy-projections are fat, for efficient vertical ray shooting queries, (ii) point enclosure—preprocess a set C of n convex simply-shaped fat objects in the plane, so that the k objects containing a query point p can be reported efficiently, (iii) bounded-size range searching— preprocess a set C of n convex fat polygons, so that the k objects intersecting a “not-too-large” query polygon can be reported efficiently, and (iv) bounded-size segment shooting—preprocess a set C as in (iii), so that the first object (if exists) hit by a “not-too-long” oriented query segment can be found efficiently. For the first three problems we construct data structures of size O(λ_s(n)log³n), where s is the maximum number of intersections between the boundaries of the (xy-projections) of any pair of objects, and λ_s(n) is the maximum length of (n, s) Davenport-Schinzel sequences. The data structure for the fourth problem is of size O(λ_s(n)log²n). The query time in the first problem is O(log⁴n), the query time in the second and third problems is O(log³n + klog²n), and the query time in the fourth problem is O(log³n).

We also present a simple algorithm for computing a depth order for a set as in (i), that is based on the solution to the vertical ray shooting problem. (A depth order for , if exists, is a linear order of , such that, if K₁, K₂ and K₁ lies vertically above K₂, then K₁ precedes K₂.) Unlike the algorithm of Agarwal et al. (1995) that might output a false order when a depth order does not exist, the new algorithm is able to determine whether such an order exists, and it is often more efficient in practical situations than the former algorithm.     

A competitive algorithm in searching for many edges in a hypergraph

We give a competitive algorithm to identify all d defective edges in a hypergraph with d unknown. Damaschke did the d=1 case for 2-graphs, Triesch extended the d=1 case to r-graphs, and Johann did the general d case for 2-graphs. So ours is the first attempt to solve the searching for defective edges problem in its full generality. Further, all the above three papers assumed d known. We give a competitive algorithm where d is unknown.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Hyphenation of column liquid chromatography and Raman spectroscopy via a liquid-core waveguide: chemometrical elimination of spectral eluent background

In column liquid chromatography (LC) coupled to conventional Raman spectroscopy (RS) removal of the spectral background of the eluent is often demanding, because of the strong signals of the organic modifier. A new chemometrical method is proposed, called the eluent background subtraction (EBS) method, which can correct for small shape and intensity differences of the eluent spectra. The variations in the eluent spectra are modelled using principal component analysis (PCA). The PCA loading vectors are subsequently used for eluent background correction of the elution spectra of the analyte. The loading vectors are fitted under these spectra by an asymmetric least-squares method. This method was successfully applied under various experimental conditions and performed much better than conventional background correction methods. Analyte detectability was improved by (weighted) averaging of all elution spectra and smoothing via a p-spline function.     

Fractionation of the human plasma proteome for monoclonal antibody proteomics‐based biomarker discovery 2: Antigen identification by dot‐blot array screening

Immunization with complex mixtures, like the human plasma resulted in the generation of cloned mAb libraries (PlasmaScan? and QuantiPlasma? libraries, with >1000 individual mAbs) reacting with a nonredundant set of antigenic epitopes. mAb proteomics refers to quasi‐hypothesis‐free profiling of plasma samples with nascent or cloned mAb libraries for the discovery of disease‐specific biomarkers. Once mAbs with biomarker potential have been identified, the next task is the determination of cognate antigens recognized by the respective mAbs. To determine the cognate protein antigen corresponding to each individual mAbs in the cloned mAb libraries, we have separated human plasma by consecutive steps of desalting and various chromatography procedures. The process resulted in 783 fractions, which we termed “Analyte Library” (AL). The AL represents the human plasma proteome in relatively low‐protein complexity fractions. Here, to determine the utility of the AL, we selected ten plasma proteins and checked for their presence in the fractions. Among the ten cases, the distribution of four selected plasma proteins matched expectations, as these proteins were present only in a few fractions corresponding to their physical, chemical, and biochemical properties. However, in six cases, we observed “smear” ‐like distribution or complete absence of the proteins, suggesting that protein–protein interactions or protein variants may alter the observed plasma distribution profiles. Nevertheless, we conclude that the AL is an efficient, high throughput tool to complement the mAb biomarker discovery process with cognate protein antigen identification for each mAbs.     

Histone deacetylase (HDAC) inhibitor curcumin upregulates mitochondrial uncoupling protein1 (UCP1) and mitochondrial function in brown adipocytes,in-silico study and screening natural drug library

Mitochondrial dysfunction has been associated with diverse pathological conditions globally. Specifically, in adipose tissues, mitochondrial dysfunction is the primary cause of obesity and obesity-related illnesses. An existing drugs such as atorvastatin and other lipid-lowering drugs demonstrated adverse effects and initiated other diseases. Thus, we need to explore new methods to prevent and treat obesity. In this study, we used the cell screening method to identify several natural compounds that increase adipocyte UCP1 gene expression. The identified drug Curcumin was evaluated in cell models and the In-silico model. We found curcumin is an active compound of turmeric belonging to Zingiberaceae (ginger family), which activates the Nrf2 mechanism. Curcumin potentially endorses the expression of UCP1 in the brown adipocyte in vitro cellular model. Curcumin plays an important role that modulating mitochondrial function and improving mitochondrial DNA quantification, ATP production, and cell viability. We have established an efficient in vitro cell experiment system to study the metabolic regulation of UCP1. The in-silico model revealed curcumin-UCP1 interaction. Curcumin, via enhancing mitochondrial activity, could be a helpful therapeutic molecule against metabolic disorders or obesity-related diseases. Curcumin will be the subject of more research in both human and murine models, which will provide novel therapeutic pathways for the treatment of metabolic illnesses by modulating the control of mitochondrial function.     

Prediction of stable BC3N2 monolayer from first-principles calculations: Stoichiometry,crystal structure,electronic and adsorption properties

In this paper, a novel BC₃N₂ monolayer has been found with a graphene-like structure using the developed particle swarm optimization algorithm in combination with ab initio calculations. The predicted structure meets the thermodynamical, dynamical, and mechanical stability requirements. Interestingly, the BC₃N₂ plane shows a metallic character. Importantly, BC₃N₂ has an in-plane stiffness comparable to that of graphene. We have also investigated the adsorption characteristics of CO₂ on pristine monolayer and Mo functionalized monolayer using density functional theory. Subsequently, electronic structures of the interacting systems (CO₂ molecule and substrates) have been preliminarily explored. The results show that Mo/BC₃N₂ has a stronger adsorption capacity towards CO₂ comparing with the pristine one, which can provide a reference for the further study of the CO₂ reduction mechanism on the transition metal-functionalized surface as well as the new catalyst’s design.     

气相色谱-质谱结合活数据库法测定煤直接液化加氢改质油中C7C9馏分的组成

采用中心切割二维气相色谱,以PONA色谱柱为一维预分析柱与氢火焰离子检测器连接,以DB-35MS色谱柱为二维分析柱与MS连接,对煤直接液化加氢改质油中C7~C9馏分进行了分离与分析,并将质谱谱库检索和活数据库法相结合对60种组分进行了定性分析。同时采用标准物质和烃类化合物在PONA柱上的保留规律对上述定性结果作了验证。还采用面积归一化方法对油样中各化合物进行了定量分析和碳数分布以及族组成分析,其中C8及C9的化合物含量分别为32.3%和51.7%,主要族组成为环烷烃(77.3%)和正构烷烃(9.63%)。