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Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
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Coordination compounds and complexes exhibit different colors, geometries, and magnetic behavior, depending on the metal atom/ion and ligands from which they are composed. In an attempt to explain the bonding and structure of coordination complexes, Linus Pauling proposed the valence bond theory, or VBT, using the concepts of hybridization and the overlapping of the atomic orbitals. According to VBT, the central metal atom or ion (Lewis acid) hybridizes to provide empty orbitals of suitable...
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In most main group element compounds, the valence electrons of the isolated atoms combine to form chemical bonds that satisfy the octet rule. For instance, the four valence electrons of carbon overlap with electrons from four hydrogen atoms to form CH4. The one valence electron leaves sodium and adds to the seven valence electrons of chlorine to form the ionic formula unit NaCl (Figure 1a). Transition metals do not normally bond in this fashion. They primarily form coordinate covalent bonds, a...
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Complex microtubule structures are present in resting cells and in dividing cells. In resting cells, they are responsible for maintaining the cellular architecture, tracks for intracellular transport, positioning of organelles, assembly of cilia and flagella. They mediate the bipolar spindle assembly for chromosomal segregation and positioning of the cell division plate in dividing cells. The formation of microtubule complex structures depends on the cell type, cell stage, and cell function.
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Synthesis of Information-bearing Peptoids and their Sequence-directed Dynamic Covalent Self-assembly
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Theoretical and computational methodologies for understanding coordination self-assembly complexes.

Satoshi Takahashi1, Satoru Iuchi2, Shuichi Hiraoka1

  • 1Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan. ghnr5571@g.ecc.u-tokyo.ac.jp.

Physical Chemistry Chemical Physics : PCCP
|April 13, 2023
PubMed
Summary
This summary is machine-generated.

This perspective introduces three computational methods—quantum chemical modeling, molecular dynamics, and reaction network analysis—to understand molecular-level coordination self-assembly. These techniques offer complementary insights to experimental studies for capturing complex self-assembly processes.

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Area of Science:

  • Chemistry
  • Computational Chemistry
  • Materials Science

Background:

  • Coordination self-assembly is crucial for developing advanced materials.
  • Understanding self-assembly at the molecular level is challenging.
  • Existing methods may not fully capture dynamic processes.

Purpose of the Study:

  • To present theoretical and computational methods for studying coordination self-assembly.
  • To bridge the gap between molecular interactions and macroscopic assembly.
  • To highlight the complementary nature of computational and experimental approaches.

Main Methods:

  • Quantum chemical modeling: Explores electronic structures and metal-ligand interactions.
  • Molecular dynamics: Simulates the movement and interactions of molecules over time.
  • Reaction network analysis: Maps and analyzes the pathways of self-assembly reactions.

Main Results:

  • These methods provide insights across different scales, from bonding to global assembly.
  • Each method offers unique perspectives on the coordination self-assembly process.
  • Computational approaches enhance the interpretation and design of experiments.

Conclusions:

  • Theoretical and computational methods are essential tools for understanding coordination self-assembly.
  • Integrating these methods with experiments provides a comprehensive view.
  • This perspective offers a framework for future research in self-assembling systems.