Tanvi, Mohd Tauheed Ilyas, G. S. S. Saini, Anamika Mukhopadhyay
{"title":"探索显性相互作用:通过DFT和从头算研究揭示可可碱-水配合物的稳定结构","authors":"Tanvi, Mohd Tauheed Ilyas, G. S. S. Saini, Anamika Mukhopadhyay","doi":"10.1007/s00894-025-06309-8","DOIUrl":null,"url":null,"abstract":"<div><h3>Context</h3><p>Solute-solvent interactions are crucial for life processes, as biological reactions primarily take place in liquid environments. Water, owing to its remarkable capacity for hydrogen bonding, plays a pivotal role as a solvent in these biological systems. This study computationally investigates the hydration of theobromine, a molecule with significant therapeutic potential and a favorable safety profile. It focuses on the intermolecular interactions within 1:1 theobromine-water complexes in order to provide a comprehensive identification of the potential interaction sites for water when theobromine is dissolved in it. In addition, the research extends to investigate species with up to three water molecules to explore the potential for cooperative binding phenomena.</p><h3>Methods</h3><p>In this work, we have employed MP2/6-311++G(d,p) and <span>\\(\\omega \\)</span>B97XD/6-311++G(d,p) levels of theory within Gaussian09 to optimize geometries and calculate the energies of theobromine-water complexes. Eight stationary points have been identified on the 1:1 theobromine-water potential energy surface, with the majority exhibiting dual hydrogen bond motifs and deviations from linearity. The global minimum structure is characterized by the simultaneous presence of O-H—O and N-H—O hydrogen bonds, with interaction energies of 7.78 kcal/mol and 9.29 kcal/mol determined at the MP2/6-311++G(d,p) and <span>\\(\\omega \\)</span>B97XD/6-311++G(d,p) levels of theory, respectively. Natural bond orbital (NBO) analysis at the MP2/6-311++G(d,p) level has been used to quantify donor-acceptor charges and hyperconjugation energies. A linear correlation between interaction energy, charge density, and bond length elongation has been observed, highlighting the intricate interplay of these key parameters. To investigate cooperative hydrogen bonding, we have modeled complexes with up to three water molecules. Weak interactions have been further characterized using atoms in molecules (AIM) analysis and reduced density gradient (RDG) approach. We have found that increasing the hydration up to two water molecules significantly reduces the tautomerization barrier from 46.09 to 20.47 kcal/mol.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 3","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Exploring the dominant interactions: unveiling the stable structure of theobromine-water complexes through DFT and ab initio investigations\",\"authors\":\"Tanvi, Mohd Tauheed Ilyas, G. S. S. Saini, Anamika Mukhopadhyay\",\"doi\":\"10.1007/s00894-025-06309-8\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Context</h3><p>Solute-solvent interactions are crucial for life processes, as biological reactions primarily take place in liquid environments. Water, owing to its remarkable capacity for hydrogen bonding, plays a pivotal role as a solvent in these biological systems. This study computationally investigates the hydration of theobromine, a molecule with significant therapeutic potential and a favorable safety profile. It focuses on the intermolecular interactions within 1:1 theobromine-water complexes in order to provide a comprehensive identification of the potential interaction sites for water when theobromine is dissolved in it. In addition, the research extends to investigate species with up to three water molecules to explore the potential for cooperative binding phenomena.</p><h3>Methods</h3><p>In this work, we have employed MP2/6-311++G(d,p) and <span>\\\\(\\\\omega \\\\)</span>B97XD/6-311++G(d,p) levels of theory within Gaussian09 to optimize geometries and calculate the energies of theobromine-water complexes. Eight stationary points have been identified on the 1:1 theobromine-water potential energy surface, with the majority exhibiting dual hydrogen bond motifs and deviations from linearity. The global minimum structure is characterized by the simultaneous presence of O-H—O and N-H—O hydrogen bonds, with interaction energies of 7.78 kcal/mol and 9.29 kcal/mol determined at the MP2/6-311++G(d,p) and <span>\\\\(\\\\omega \\\\)</span>B97XD/6-311++G(d,p) levels of theory, respectively. Natural bond orbital (NBO) analysis at the MP2/6-311++G(d,p) level has been used to quantify donor-acceptor charges and hyperconjugation energies. A linear correlation between interaction energy, charge density, and bond length elongation has been observed, highlighting the intricate interplay of these key parameters. To investigate cooperative hydrogen bonding, we have modeled complexes with up to three water molecules. Weak interactions have been further characterized using atoms in molecules (AIM) analysis and reduced density gradient (RDG) approach. 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Exploring the dominant interactions: unveiling the stable structure of theobromine-water complexes through DFT and ab initio investigations
Context
Solute-solvent interactions are crucial for life processes, as biological reactions primarily take place in liquid environments. Water, owing to its remarkable capacity for hydrogen bonding, plays a pivotal role as a solvent in these biological systems. This study computationally investigates the hydration of theobromine, a molecule with significant therapeutic potential and a favorable safety profile. It focuses on the intermolecular interactions within 1:1 theobromine-water complexes in order to provide a comprehensive identification of the potential interaction sites for water when theobromine is dissolved in it. In addition, the research extends to investigate species with up to three water molecules to explore the potential for cooperative binding phenomena.
Methods
In this work, we have employed MP2/6-311++G(d,p) and \(\omega \)B97XD/6-311++G(d,p) levels of theory within Gaussian09 to optimize geometries and calculate the energies of theobromine-water complexes. Eight stationary points have been identified on the 1:1 theobromine-water potential energy surface, with the majority exhibiting dual hydrogen bond motifs and deviations from linearity. The global minimum structure is characterized by the simultaneous presence of O-H—O and N-H—O hydrogen bonds, with interaction energies of 7.78 kcal/mol and 9.29 kcal/mol determined at the MP2/6-311++G(d,p) and \(\omega \)B97XD/6-311++G(d,p) levels of theory, respectively. Natural bond orbital (NBO) analysis at the MP2/6-311++G(d,p) level has been used to quantify donor-acceptor charges and hyperconjugation energies. A linear correlation between interaction energy, charge density, and bond length elongation has been observed, highlighting the intricate interplay of these key parameters. To investigate cooperative hydrogen bonding, we have modeled complexes with up to three water molecules. Weak interactions have been further characterized using atoms in molecules (AIM) analysis and reduced density gradient (RDG) approach. We have found that increasing the hydration up to two water molecules significantly reduces the tautomerization barrier from 46.09 to 20.47 kcal/mol.
期刊介绍:
The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling.
Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry.
Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.