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Polymers
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Computational Chemistry
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Computational Chemistry

A special issue of Polymers (ISSN 2073-4360).

Deadline for manuscript submissions: closed (30 June 2014) | Viewed by 46782

Special Issue Editor

Prof. Dr. Davide Moscatelli

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Guest Editor
Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, 20131 Milano, Italy
Interests: chemical reaction engineering; polymer reaction engineering

Special Issue Information

Dear Colleagues,

The advent of powerful analytic techniques, such as pulsed laser polymerization (PLP) combined with size exclusion chromatography (SEC), has enabled the reliable and accurate estimation of propagation rate coefficients in free radical polymerization (FRP). However, the measurement of kinetic parameters, such as activation energies and rate coefficients, is time consuming and complicated by difficult experimental conditions as well as secondary reaction mechanisms that occur simultaneously. As a result, it is often impossible to focus on individual contributions in isolation from the whole kinetic scheme. On the other hand, Computational Chemistry can be used to elucidate mechanisms and reaction pathways to complement experimental analyses. In fact, the rapid and continual increase in computer power has enabled the combination of Quantum Chemistry, Semiempirical Methods, and Molecular Dynamics to determine with satisfactory accuracy different properties such as molecular geometries (bond lengths, bond angles, and torsional angles), energetic reaction profiles, vibrational frequencies of molecular species, transition state structures, and reaction frequency factors.

Prof. Dr. Davide Moscatelli
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • quantum chemistry
  • free Radical polymerization
  • kinetics
  • modeling
  • molecular dynamics
  • level of theory

Published Papers (4 papers)

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Research

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3509 KiB  
Article
Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins
by Jay Eifler, Paul Rulis, Rex Tai and Wai-Yim Ching
Polymers 2014, 6(2), 491-514; https://doi.org/10.3390/polym6020491 - 18 Feb 2014
Cited by 12 | Viewed by 7269
Abstract
Collagen molecules are the primary structural proteins of many biological systems. Much progress has been made in the study of the structure and function of collagen, but fundamental understanding of its electronic structures at the atomic level is still lacking. We present the [...] Read more.
Collagen molecules are the primary structural proteins of many biological systems. Much progress has been made in the study of the structure and function of collagen, but fundamental understanding of its electronic structures at the atomic level is still lacking. We present the results of electronic structure and bonding calculations of a specific model of type I collagen using the density functional theory-based method. Information on density of states (DOS), partial DOS, effective charges, bond order values, and intra- and inter-molecular H-bonding are obtained and discussed. We further devised an amino-acid-based potential method (AAPM) to circumvent the full self-consistent field (SCF) calculation that can be applied to large proteins. The AAPM is validated by comparing the results with the full SCF calculation of the whole type I collagen model with three strands. The calculated effective charges on each atom in the model retained at least 95% accuracy. This technique provides a viable and efficient way to study the electronic structure of large complex biomaterials at the ab initio level. Full article
(This article belongs to the Special Issue Computational Chemistry)
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Review

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1210 KiB  
Review
On the Use of Quantum Chemistry for the Determination of Propagation, Copolymerization, and Secondary Reaction Kinetics in Free Radical Polymerization
by Evangelos Mavroudakis, Danilo Cuccato and Davide Moscatelli
Polymers 2015, 7(9), 1789-1819; https://doi.org/10.3390/polym7091483 - 17 Sep 2015
Cited by 42 | Viewed by 9316
Abstract
Throughout the last 25 years, computational chemistry based on quantum mechanics has been applied to the investigation of reaction kinetics in free radical polymerization (FRP) with growing interest. Nowadays, quantum chemistry (QC) can be considered a powerful and cost-effective tool for the kinetic [...] Read more.
Throughout the last 25 years, computational chemistry based on quantum mechanics has been applied to the investigation of reaction kinetics in free radical polymerization (FRP) with growing interest. Nowadays, quantum chemistry (QC) can be considered a powerful and cost-effective tool for the kinetic characterization of many individual reactions in FRP, especially those that cannot yet be fully analyzed through experiments. The recent focus on copolymers and systems where secondary reactions play a major role has emphasized this feature due to the increased complexity of these kinetic schemes. QC calculations are well-suited to support and guide the experimental investigation of FRP kinetics as well as to deepen the understanding of polymerization mechanisms. This paper is intended to provide an overview of the most relevant QC results obtained so far from the investigation of FRP. A comparison between computational results and experimental data is given, whenever possible, to emphasize the performances of the two approaches in the prediction of kinetic data. This work provides a comprehensive database of reaction rate parameters of FRP to assist in the development of advanced models of polymerization and experimental studies on the topic. Full article
(This article belongs to the Special Issue Computational Chemistry)
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4781 KiB  
Review
Intrinsically Disordered Proteins: Where Computation Meets Experiment
by Virginia M. Burger, Thomas Gurry and Collin M. Stultz
Polymers 2014, 6(10), 2684-2719; https://doi.org/10.3390/polym6102684 - 23 Oct 2014
Cited by 48 | Viewed by 15945
Abstract
Proteins are heteropolymers that play important roles in virtually every biological reaction. While many proteins have well-defined three-dimensional structures that are inextricably coupled to their function, intrinsically disordered proteins (IDPs) do not have a well-defined structure, and it is this lack of structure [...] Read more.
Proteins are heteropolymers that play important roles in virtually every biological reaction. While many proteins have well-defined three-dimensional structures that are inextricably coupled to their function, intrinsically disordered proteins (IDPs) do not have a well-defined structure, and it is this lack of structure that facilitates their function. As many IDPs are involved in essential cellular processes, various diseases have been linked to their malfunction, thereby making them important drug targets. In this review we discuss methods for studying IDPs and provide examples of how computational methods can improve our understanding of IDPs. We focus on two intensely studied IDPs that have been implicated in very different pathologic pathways. The first, p53, has been linked to over 50% of human cancers, and the second, Amyloid-β (Aβ), forms neurotoxic aggregates in the brains of patients with Alzheimer’s disease. We use these representative proteins to illustrate some of the challenges associated with studying IDPs and demonstrate how computational tools can be fruitfully applied to arrive at a more comprehensive understanding of these fascinating heteropolymers. Full article
(This article belongs to the Special Issue Computational Chemistry)
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1108 KiB  
Review
Atomistic Studies of Mechanical Properties of Graphene
by Guoxin Cao
Polymers 2014, 6(9), 2404-2432; https://doi.org/10.3390/polym6092404 - 22 Sep 2014
Cited by 158 | Viewed by 13286
Abstract
Recent progress of simulations/modeling at the atomic level has led to a better understanding of the mechanical behaviors of graphene, which include the linear elastic modulus E, the nonlinear elastic modulus D, the Poisson’s ratio ν, the intrinsic strength σ [...] Read more.
Recent progress of simulations/modeling at the atomic level has led to a better understanding of the mechanical behaviors of graphene, which include the linear elastic modulus E, the nonlinear elastic modulus D, the Poisson’s ratio ν, the intrinsic strength σint and the corresponding strain εint as well as the ultimate strain εmax (the fracture strain beyond which the graphene lattice will be unstable). Due to the two-dimensional geometric characteristic, the in-plane tensile response and the free-standing indentation response of graphene are the focal points in this review. The studies are based on multiscale levels: including quantum mechanical and classical molecular dynamics simulations, and parallel continuum models. The numerical studies offer useful links between scientific research with engineering application, which may help to fulfill graphene potential applications such as nano sensors, nanotransistors, and other nanodevices. Full article
(This article belongs to the Special Issue Computational Chemistry)
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