A reliable model for assessment of melting points of cyclic hydrocarbons containing complex molecular structures, isomers and stereoisomers

2020 ◽  
Vol 521 ◽  
pp. 112692
Author(s):  
Mohammad Hossein Keshavarz ◽  
Narjes Khaton Maghsoodi ◽  
Arash Shokrollahi
2014 ◽  
Vol 716-717 ◽  
pp. 180-183
Author(s):  
Hong Yin Cao ◽  
Rui Wang

A quantitative structure–property relationship (QSPR) model for predicting the standard net heat of combustion () was developed based on the ant colony optimization (ACO) method coupled with the partial least square (PLS) for variable selection. Five molecular descriptors were screened out as the parameters of the model, which were finally constructed using multi-linear regression (MLR) method. A reliable model of five parameters for predicting the of esters was established, which can provide some help for engineering to predict the based on only their molecular structures.


2016 ◽  
Vol 427 ◽  
pp. 27-34 ◽  
Author(s):  
Behzad Nazari ◽  
Masood Hamadanian ◽  
Mohammad Hossein Keshavarz ◽  
Javad Rezaei

1971 ◽  
Vol 75 (9) ◽  
pp. 1264-1271 ◽  
Author(s):  
Richard H. Boyd ◽  
Shiv N. Sanwal ◽  
Shahrokh Shary-Tehrany ◽  
Donal McNally

2019 ◽  
Author(s):  
ganesh sivaraman ◽  
Nicholas Jackson ◽  
Benjamin Sanchez-Lengeling ◽  
Alvaro Vazquez-Mayagoitia ◽  
Alan Aspuru-Guzik ◽  
...  

<p>The ability to predict multi-molecule processes, using only knowledge of single molecule structure, stands as a grand challenge for molecular modeling. Methods capable of predicting melting points (MP) solely from chemical structure represent a canonical example, and are highly desirable in many crucial industrial applications. In this work, we explore a data-driven approach utilizing machine learning (ML) techniques to predict and understand the MP of molecules. Several experimental databases are aggregated from the literature to design a low-bias dataset that includes 3D structural and quantum-chemical properties. Using experimental and polymorph-induced uncertainties, we derive a tenable lower limit for MP prediction accuracy, and apply graph neural networks and Gaussian processes to predict MP competitive with these error bounds. To further understand how MP correlates with molecular structure, we employ several semi-supervised and unsupervised ML techniques. First, we use unsupervised clustering methods to identify classes of molecules, their common fragments, and expected errors for each data set. We then build molecular geometric spaces shaped by MP with a semi-supervised variational autoencoder and graph embedding spaces, and apply graph attribution methods to highlight atom-level contributions to MP within the datasets. Overall, this work serves as a case study of how to employ a diversified ML toolkit to predict and understand correlations between molecular structures and thermophysical properties of interest.</p>


2019 ◽  
Author(s):  
ganesh sivaraman ◽  
Nicholas Jackson ◽  
Benjamin Sanchez-Lengeling ◽  
Alvaro Vazquez-Mayagoitia ◽  
Alan Aspuru-Guzik ◽  
...  

<p>The ability to predict multi-molecule processes, using only knowledge of single molecule structure, stands as a grand challenge for molecular modeling. Methods capable of predicting melting points (MP) solely from chemical structure represent a canonical example, and are highly desirable in many crucial industrial applications. In this work, we explore a data-driven approach utilizing machine learning (ML) techniques to predict and understand the MP of molecules. Several experimental databases are aggregated from the literature to design a low-bias dataset that includes 3D structural and quantum-chemical properties. Using experimental and polymorph-induced uncertainties, we derive a tenable lower limit for MP prediction accuracy, and apply graph neural networks and Gaussian processes to predict MP competitive with these error bounds. To further understand how MP correlates with molecular structure, we employ several semi-supervised and unsupervised ML techniques. First, we use unsupervised clustering methods to identify classes of molecules, their common fragments, and expected errors for each data set. We then build molecular geometric spaces shaped by MP with a semi-supervised variational autoencoder and graph embedding spaces, and apply graph attribution methods to highlight atom-level contributions to MP within the datasets. Overall, this work serves as a case study of how to employ a diversified ML toolkit to predict and understand correlations between molecular structures and thermophysical properties of interest.</p>


Author(s):  
Cecil E. Hall

The visualization of organic macromolecules such as proteins, nucleic acids, viruses and virus components has reached its high degree of effectiveness owing to refinements and reliability of instruments and to the invention of methods for enhancing the structure of these materials within the electron image. The latter techniques have been most important because what can be seen depends upon the molecular and atomic character of the object as modified which is rarely evident in the pristine material. Structure may thus be displayed by the arts of positive and negative staining, shadow casting, replication and other techniques. Enhancement of contrast, which delineates bounds of isolated macromolecules has been effected progressively over the years as illustrated in Figs. 1, 2, 3 and 4 by these methods. We now look to the future wondering what other visions are waiting to be seen. The instrument designers will need to exact from the arts of fabrication the performance that theory has prescribed as well as methods for phase and interference contrast with explorations of the potentialities of very high and very low voltages. Chemistry must play an increasingly important part in future progress by providing specific stain molecules of high visibility, substrates of vanishing “noise” level and means for preservation of molecular structures that usually exist in a solvated condition.


Author(s):  
Patricia G. Arscott ◽  
Gil Lee ◽  
Victor A. Bloomfield ◽  
D. Fennell Evans

STM is one of the most promising techniques available for visualizing the fine details of biomolecular structure. It has been used to map the surface topography of inorganic materials in atomic dimensions, and thus has the resolving power not only to determine the conformation of small molecules but to distinguish site-specific features within a molecule. That level of detail is of critical importance in understanding the relationship between form and function in biological systems. The size, shape, and accessibility of molecular structures can be determined much more accurately by STM than by electron microscopy since no staining, shadowing or labeling with heavy metals is required, and there is no exposure to damaging radiation by electrons. Crystallography and most other physical techniques do not give information about individual molecules.We have obtained striking images of DNA and RNA, using calf thymus DNA and two synthetic polynucleotides, poly(dG-me5dC)·poly(dG-me5dC) and poly(rA)·poly(rU).


Author(s):  
Nobutaka Hirokawa

In this symposium I will present our studies about the molecular architecture and function of the cytomatrix of the nerve cells. The nerve cell is a highly polarized cell composed of highly branched dendrites, cell body, and a single long axon along the direction of the impulse propagation. Each part of the neuron takes characteristic shapes for which the cytoskeleton provides the framework. The neuronal cytoskeletons play important roles on neuronal morphogenesis, organelle transport and the synaptic transmission. In the axon neurofilaments (NF) form dense arrays, while microtubules (MT) are arranged as small clusters among the NFs. On the other hand, MTs are distributed uniformly, whereas NFs tend to run solitarily or form small fascicles in the dendrites Quick freeze deep etch electron microscopy revealed various kinds of strands among MTs, NFs and membranous organelles (MO). These structures form major elements of the cytomatrix in the neuron. To investigate molecular nature and function of these filaments first we studied molecular structures of microtubule associated proteins (MAP1A, MAP1B, MAP2, MAP2C and tau), and microtubules reconstituted from MAPs and tubulin in vitro. These MAPs were all fibrous molecules with different length and formed arm like projections from the microtubule surface.


1964 ◽  
Vol 12 (01) ◽  
pp. 232-261 ◽  
Author(s):  
S Sasaki ◽  
T Takemoto ◽  
S Oka

SummaryTo demonstrate whether the intravascular precipitation of fibrinogen is responsible for the toxicity of heparinoid, the relation between the toxicity of heparinoid in vivo and the precipitation of fibrinogen in vitro was investigated, using dextran sulfate of various molecular weights and various heparinoids.1. There are close relationships between the molecular weight of dextran sulfate, its toxicity, and the quantity of fibrinogen precipitated.2. The close relationship between the toxicity and the precipitation of fibrinogen found for dextran sulfate holds good for other heparinoids regardless of their molecular structures.3. Histological findings suggest strongly that the pathological changes produced with dextran sulfate are caused primarily by the intravascular precipitates with occlusion of the capillaries.From these facts, it is concluded that the precipitates of fibrinogen with heparinoid may be the cause or at least the major cause of the toxicity of heparinoid.4. The most suitable molecular weight of dextran sulfate for clinical use was found to be 5,300 ~ 6,700, from the maximum value of the product (LD50 · Anticoagulant activity). This product (LD50 · Anticoagulant activity) can be employed generally to assess the comparative merits of various heparinoids.5. Clinical use of the dextran sulfate prepared on this basis gave satisfactory results. No severe reaction was observed. However, two delayed reactions, alopecia and thrombocytopenia, were observed. These two reactions seem to come from the cause other than intravascular precipitation.


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