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DFT Physical chemistry Quantum chemical calculation Metal complex Self-assembly Machine learning
An automated conformational search method was employed to efficiently determine the stable conformers and weak hydrogen bonds of a flexible tripeptide coordinated with a solitary metal(II) ion in an aqueous environment. Quantum chemical calculations were performed to investigate the tendency of octahedral coordination formation between different metal(II) ions and various coordination models (ammonia molecule, chelate molecule, and flexible tripeptide). The octahedral coordination was analyzed by decomposing it into tridentate, bidentate, and monodentate coordination model complexes to assess their formation propensities and conformational properties. Additionally, population analysis, including electrostatic potential mapping and natural population analysis, was performed to identify the unique properties of the Ni(II) ion in forming octahedral coordination in crystals and to explore the potential of other metal(II) ions for self-assembling novel coordination configurations in peptide-metal compounds. Two common hydrogen bonding interactions were examined by using artificial forces to facilitate dissociation or reinforcement.
Niobocene hydride–silyl complexes exhibit intriguing structural characteristics with the potential for direct hydride/silyl exchange, where hydride migration plays a crucial role during conformational interconversion. In this study, quantum chemical calculations were utilized to investigate the transformation pathways involved in hydride/silyl exchange in niobocene trihydride complexes with various dichlorosilanes, including SiCl2Me2, SiCl2iPr2, and SiCl2MePh ligands. The conformational changes and hydride shifts within these niobocene hydride–silyl complexes were examined, and key intermediates were identified. Electronic wavefunction analysis provided insights into the coordination configurations and the nature of inter-ligand interactions. Interaction region indicator (IRI) analysis revealed Van der Waals interactions between chloride atoms and cyclopentadienyl rings, as well as between chloride atoms and Me, iPr, and Ph groups. Notably, distinct interactions between hydride ligands, including those from Si-H moieties and coordinated hydrogen atoms, were observed. Both lateral and central conformations, with respect to silicon coordination to the niobium center, were considered. This study enhances the understanding of intermediate conformations in the hydride/silyl exchange process and provides a detailed characterization of inter-ligand interactions, offering valuable insights for analyzing metallocene complexes with organic ligand coordination.
A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination.
This study presents a quantum chemical investigation into the structural analysis and calculated Raman spectra of modeled amylose with varying units of linked glucose molecules. We systematically examined the rotation of hydroxymethyl groups and intramolecular hydrogen bonds within these amylose models. Our study found that as the number of linked glucose units increases, the linear structure becomes more complex, resulting in curled, cyclic, or helical structures facilitated by establishing various intramolecular interactions. The hydroxymethyl groups were confirmed to form interactions with oxygen atoms and with hydroxymethyl and hydroxyl groups from adjacent rings in the molecular structures. We identified distinct peaks and selected specific bands applicable in various analytical contexts by comparing their calculated Raman spectra. Representative vibrational modes within selected regions were identified across the different lengths of amylose models, serving as characteristic signatures for linear and more coiled structural conformations. Our findings contribute to a deeper understanding of amylose structures and spectroscopic signatures, with implications for theoretical studies and potential applications. This work provides valuable reference points for the detailed assignment of Raman peaks of amylose structure, facilitating their application in broader research on carbohydrate structures and their associated spectroscopic properties.
A comprehensive theoretical investigation of the C3H2O potential energy surface (PES) was conducted, revealing 30 equilibrium structures (EQs), 128 transition state structures (TSs), and 35 direct dissociation channels (DCs), establishing a global reaction network comprising 101 isomerization pathways and dissociation channels. Particular focus was placed on the five most stable isomers, H2CCCO (EQ3), OC(H)CCH (EQ7), H-c-CC(O)C-H (EQ0), HCC(H)CO (EQ1), and HO-c-CCC-H (EQ12), and their reactions with water molecules. Multicomponent artificial force-induced reaction (MC-AFIR) calculations were employed to study bimolecular collisions between H2O and these stable isomers. The product distributions revealed isomer-specific reactivity patterns: EQ3 and EQ7 predominantly formed neutral species at high collision energies, EQ0 produced both ionic and neutral species, while EQ1 and EQ12 exhibited more accessible reaction pathways at lower collision energies with a propensity for spontaneous isomerization. Born–Oppenheimer Molecular Dynamics (BOMD) simulations complemented these findings, suggesting several viable products emerge from reactions with water molecules, including HCCC(OH)2H (EQ7 + H2O), OCCHCH2OH (EQ1 + H2O), and HO-c-CC(H)C(OH)-H (EQ12 + H2O). This investigation elucidates the intrinsic relationships between isomers and their potential products, formed through biomolecular collisions with water molecules, establishing a fundamental framework for future conformational and reactivity studies of the C3H2O family.
Cyanoformaldehyde [HC(O)CN], a detected interstellar molecule, exhibits potential isomeric transformations that remain incompletely understood. Understanding its conformational flexibility is crucial for predicting its reactivity in interstellar conditions. This study presents a comprehensive investigation of the complete HC(O)CN potential energy surface (PES) using the anharmonic downward distortion following (ADDF) algorithm, enabling exhaustive mapping of EQs, TSs, DCs, and connecting pathways. At the B3LYP-D3(BJ)/def2-TZVP level of theory, our analysis reveals 48 EQs, 152 TSs, and 49 DCs. We identify 80 unique isomerization pathways mediated by TS structures (EQ<i>x</i>-TS<i>n</i>-EQ<i>y</i>), complemented by 34 TS-mediated (EQ<i>a</i>-TS<i>b</i>-DC) and 40 direct (EQ<i>m</i>-DC<i>n</i>) DCs. The multicomponent artificial force induced reaction (MC-AFIR) method is employed to generate stochastic conformational ensembles comprising the most stable isomers in investigations and a single water molecule, enabling systematic analysis of product formation propensities. These findings provide a comprehensive database of conformational relationships, thermodynamic behaviors, and water-involved reactions for HC(O)CN isomers. Our analysis establishes a reference framework for predicting isomer stability, interconversion pathways, and reactivity under various conditions.
Abstract The rational design of artificial supramolecular structures with specific properties and functions hinges the comprehensive understanding of the coordination and noncovalent interactions driving self‐assembly. Herein, the self‐assembly of supramolecular systems through octahedral coordination between Ni(II) ions and a flexible tripeptide was theoretically investigated using quantum chemical calculations. These calculations utilized the B3LYP functional with the polarizable continuum model. Our results indicate that tridentate sites have a greater propensity for coordination, and that the presence of chloride anions and conformational shifts enhance bidentate and monodentate coordination. Insights into the effect of counter anions on the stability of octahedral coordination and the prerequisites for self‐assembly were gained by determining the stable conformation and potential reaction pathways of the tripeptide before and after adding chloride anions through an efficient automated conformational search. The formation of intramolecular hydrogen bonding interactions during the conformational changes was also studied using model calculations. Possible processes for initial self‐assembly of tripeptide were proposed. This study enhances the fundamental understanding of the conformational behavior of building blocks during supramolecular formation and advance the potential for constructing future bioinspired complexes.
To develop sophisticated artificial systems that are comparable to those in nature, understanding the principles controlling the assembly of flexible molecules into giant structures is essential. In this study, the metal-mediated self-assembly of a flexible tripeptide into three giant discrete complexes was analyzed using small-angle X-ray scattering along with other experimental and simulation studies. We revealed the kinetic and thermodynamic contributions during the assembly process, which resulted in the selective formation of two giant discrete structures of similar sizes in a water/acetonitrile solution. We also identified the factors that open the kinetic pathway to giant [2]-catenane structures in aqueous solutions. The formation of structures containing multiple components is generally considered kinetically unfavorable. However, our results revealed that solvent molecules and counterions kinetically initiate the formation of giant, multicomponent catenane structures in aqueous solutions.
