Independent gradient model based on Hirshfeld partition (IGMH): A new method for visual study of interactions in chemical systems

Mapping Intimacies ◽

10.26434/chemrxiv-2021-628vh ◽

2021 ◽

Author(s):

Tian Lu ◽

Qinxue Chen

Keyword(s):

Visual Analysis ◽

Weak Interactions ◽

Chem Phys ◽

Noncovalent Interaction ◽

Chemical Systems ◽

Gradient Model ◽

Atom Pairs ◽

New Variant ◽

Physical Background ◽

User Friendly

The independent gradient model (IGM) originally proposed in Phys. Chem. Chem. Phys., 19, 17928 (2017) has been increasingly popular in visual analysis of intramolecular and intermolecular interactions in recent years, and it has many clear advantages over the widely employed noncovalent interaction (NCI) method, such as intrafragment and interfragment interactions can be elegantly isolated and thus separately studied, the isosurfaces are smoother and less jaggy. However, we frequently observed that there is an evident shortcoming of IGM map in graphically studying weak interactions, that is its isosurfaces are usually too bulgy; in these cases, not only the graphical effect is poor, but also the color on some areas on the isosurfaces is inappropriate and may lead to erroneous analysis conclusions. In addition, the IGM method was originally proposed based on promolecular density, which is quite crude and does not take actual electronic structure into account. In this article, we first present a detailed overview of the IGM analysis, and then propose our new variant of IGM, namely IGM based on Hirshfeld partition of molecular density (IGMH), which replaces the free-state atomic densities involved in the IGM method with the atomic densities derived by Hirshfeld partition of actual molecular electron density. This change makes IGM have more rigorous physical background. In addition, we describe some indices defined on the top of IGM or IGMH framework to quantify contributions from various atoms or atom pairs to interaction between specific fragments. A large number of application examples in this article, including molecular and periodic systems, weak and chemical bond interactions, fully demonstrate the important value of IGMH in intuitively understanding interactions in chemical systems. Comparisons also showed that the IGMH usually has markedly better graphical effect than IGM and overcomes known problems in IGM. Currently IGMH analysis has been efficiently supported in our freely available and user-friendly wavefunction analysis code Multiwfn (http://sobereva.com/multiwfn), and a detailed tutorial is presented. We hope that IGMH will become a new popular method among chemists for exploring interactions in wide variety of chemical systems.

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Independent gradient model based on Hirshfeld partition (IGMH): A new method for visual study of interactions in chemical systems

10.26434/chemrxiv-2021-628vh-v2 ◽

2021 ◽

Author(s):

Tian Lu ◽

Qinxue Chen

Keyword(s):

Visual Analysis ◽

Weak Interactions ◽

Chem Phys ◽

Noncovalent Interaction ◽

Chemical Systems ◽

Gradient Model ◽

Atom Pairs ◽

New Variant ◽

Physical Background ◽

User Friendly

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Justifying the data analytical choice in single case research in relation to the expected data pattern

10.31234/osf.io/2b9mu ◽

2019 ◽

Author(s):

Rumen Manolov

Keyword(s):

Data Analysis ◽

Visual Analysis ◽

Multilevel Models ◽

Single Case ◽

Analytical Techniques ◽

Real Data ◽

Small Scale ◽

Data User ◽

Single Case Research ◽

User Friendly

The lack of consensus regarding the most appropriate analytical techniques for single-case experimental designs data requires justifying the choice of any specific analytical option. The current text mentions some of the arguments, provided by methodologists and statisticians, in favor of several analytical techniques. Additionally, a small-scale literature review is performed in order to explore if and how applied researchers justify the analytical choices that they make. The review suggests that certain practices are not sufficiently explained. In order to improve the reporting regarding the data analytical decisions, it is proposed to choose and justify the data analytical approach prior to gathering the data. As a possible justification for data analysis plan, we propose using as a basis the expected the data pattern (specifically, the expectation about an improving baseline trend and about the immediate or progressive nature of the intervention effect). Although there are multiple alternatives for single-case data analysis, the current text focuses on visual analysis and multilevel models and illustrates an application of these analytical options with real data. User-friendly software is also developed.

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Publisher’s Note: “A modified next reaction method for simulating chemical systems with time dependent propensities and delays” [J. Chem. Phys. 127, 214107 (2007)]

The Journal of Chemical Physics ◽

10.1063/1.2899331 ◽

2008 ◽

Vol 128 (10) ◽

pp. 109903 ◽

Cited By ~ 1

Author(s):

David F. Anderson

Keyword(s):

Chem Phys ◽

Time Dependent ◽

Reaction Method ◽

Chemical Systems

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Asymmetric Induction and Amplification in Stereodynamic Catalytic Systems by Noncovalent Interactions

Synlett ◽

10.1055/a-1274-2777 ◽

2020 ◽

Author(s):

Oliver Trapp ◽

Jan Felix Scholtes

Keyword(s):

Noncovalent Interactions ◽

Noncovalent Interaction ◽

Kinetic Properties ◽

Catalytic Systems ◽

Asymmetric Transformations ◽

Chemical Systems ◽

Chiral Induction ◽

Chiral Amplification ◽

Biochemical Systems ◽

Local Transmission

AbstractThe local transmission of chiral information by noncovalent interactions is one of the most fundamental processes broadly found in nature, i.e. in complex biochemical systems. This review summarizes our accomplishments in investigating chiral induction in stereodynamic ligands and catalysts by weak intermolecular interactions. It includes our efforts to characterize numerous stereodynamic compounds in detail with respect to their thermodynamic and kinetic properties. Furthermore, many stereolabile ligands for enantioselective catalysis are described, where directed stereoinduction afforded highly enantio- or diastereoenriched catalysts for subsequent selective asymmetric transformations. Various approaches for the dynamic enrichment of one of the catalyst’s conformers are presented, such as noncovalent interaction of the ligand with a chiral environment or a chiral solute. Finally, successful chemical systems are presented in which a process of chiral induction can be coupled with an autoinductive mechanism triggered by the chirality of its own reaction product, realizing Nature-inspired feedback loops resulting in self-amplifying, enantioselective catalytic reactions.1 Introduction2 Mapping the Stereodynamic Landscape3 Chiral Induction by Noncovalent Interactions4 Autoinduction and Chiral Amplification5 Self-Alignment and Emergence of Chirality6 Conclusion

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Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts

BMC Bioinformatics ◽

10.1186/s12859-021-04321-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

John J. Cole ◽

Bekir A. Faydaci ◽

David McGuinness ◽

Robin Shaw ◽

Rose A. Maciewicz ◽

...

Keyword(s):

Visual Analysis ◽

Service Providers ◽

Single Gene ◽

Experimental Designs ◽

Rna Seq ◽

Analysis Study ◽

Processing Pipeline ◽

Shiny App ◽

User Friendly ◽

Downstream User

Abstract Background Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed using R. Though commercial visualisation and interpretation pipelines are comprehensive, freely available pipelines are currently more limited. Results Here we demonstrate Searchlight, a freely available bulk RNA-seq visualisation and interpretation pipeline. Searchlight provides: a comprehensive statistical and visual analysis, focusing on the global, pathway and single gene levels; compatibility with most differential experimental designs irrespective of organism or experimental complexity, via three workflows; reports; and support for downstream user modification of plots via user-friendly R-scripts and a Shiny app. We show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). We demonstrate in a timed re-analysis study, that alongside a standard bulk RNA-seq processing pipeline, Searchlight can be used to complete bulk RNA-seq projects up to the point of manuscript quality figures, in under 3 h. Conclusions Compared to a manual R based analysis or current best freely available pipelines (VIPER and BioJupies), Searchlight can reduce the time and effort needed to complete bulk RNA-seq projects to manuscript level. Searchlight is suitable for bioinformaticians, service providers and bench scientists. https://github.com/Searchlight2/Searchlight2.

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Molecular Docking Using Chimera and Autodock Vina Software for Nonbioinformaticians

JMIR Bioinformatics and Biotechnology ◽

10.2196/14232 ◽

2020 ◽

Vol 1 (1) ◽

pp. e14232

Author(s):

Sania Safdar Butt ◽

Yasmin Badshah ◽

Maria Shabbir ◽

Mehak Rafiq

Keyword(s):

Molecular Docking ◽

San Francisco ◽

Target Protein ◽

Autodock Vina ◽

Protein Database ◽

Computational Docking ◽

Chemical Systems ◽

Modern Drug ◽

User Friendly ◽

Ucsf Chimera

In the field of drug discovery, many methods of molecular modeling have been employed to study complex biological and chemical systems. Experimental strategies are integrated with computational approaches for the identification, characterization, and development of novel drugs and compounds. In modern drug designing, molecular docking is an approach that explores the confirmation of a ligand within the binding site of a macromolecule. To date, many software and tools for docking have been employed. AutoDock Vina (in UCSF [University of California, San Francisco] Chimera) is one of the computationally fastest and most accurate software employed in docking. In this paper, a sequential demonstration of molecular docking of the ligand fisetin with the target protein Akt has been provided, using AutoDock Vina in UCSF Chimera 1.12. The first step involves target protein ID retrieval from the protein database, the second step involves visualization of the protein structure in UCSF Chimera, the third step involves preparation of the target protein for docking, the fourth step involves preparation of the ligand for docking, the fifth step involves docking of the ligand and the target protein as Mol.2 files in Chimera by using AutoDock Vina, and the final step involves interpretation and analysis of the docking results. By following the guidelines and steps outlined in this paper, researchers with no previous background in bioinformatics research can perform computational docking in an easier and more user-friendly manner.

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Halogen Bonding: A Halogen-Centered Noncovalent Interaction Yet to Be Understood

Inorganics ◽

10.3390/inorganics7030040 ◽

2019 ◽

Vol 7 (3) ◽

pp. 40 ◽

Cited By ~ 37

Author(s):

Pradeep Varadwaj ◽

Arpita Varadwaj ◽

Helder Marques

Keyword(s):

Electron Density ◽

Weak Interactions ◽

Early Recognition ◽

Noncovalent Interactions ◽

Covalent Bond ◽

Halogen Bonding ◽

Noncovalent Interaction ◽

Type I ◽

Type Ii ◽

Halogen Bonds

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site.

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van der Waals Potential: An Important Complement to Molecular Electrostatic Potential in Studying Intermolecular Interactions

10.26434/chemrxiv.12148572 ◽

2020 ◽

Author(s):

Tian Lu ◽

Qinxue Chen

Keyword(s):

Electrostatic Potential ◽

Molecular Electrostatic Potential ◽

Visual Analysis ◽

Weak Interactions ◽

Van Der Waals ◽

Dynamics Simulation ◽

Practical Implementation ◽

Spatial Distribution Function ◽

Definition Of

Electrostatic and van der Waals (vdW) interactions are two major components of intermolecular weak interactions. Electrostatic potential has been a very popular function in revealing electrostatic interaction between the system under study and other species, while the role of vdW potential is less recognized and has long been ignored. In this paper, we explicitly present definition of vdW potential, describe its practical implementation, and demonstrate its important value by visual analysis and comparing it with spatial distribution function obtained via molecular dynamics simulation. We hope this work can arouse researchers' attention to van der Waals potential and promote its application in practical studies of weak interaction. Calculation, visualization and quantitative analysis of the vdW potential have been supported by our freely available code Multiwfn (http://sobereva.com/multiwfn).

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