Doungous Sale, Alhadji Malloum, Mama Nsangou, Jean Jules Fifen, Jeanet Conradie
{"title":"苯硼酸的微水化及其水化自由能。","authors":"Doungous Sale, Alhadji Malloum, Mama Nsangou, Jean Jules Fifen, Jeanet Conradie","doi":"10.1007/s00894-025-06436-2","DOIUrl":null,"url":null,"abstract":"<div><h3>\n <b>Context</b>\n </h3><p>Understanding the interactions of phenylboronic acid with its surrounding water molecules is essential for several applications in solvated systems. In the present work, we investigated the microhydration of the phenylboronic acid (PBA) and calculated its hydration free energy using the cluster continuum solvation model. Microhydration of PBA has not been investigated previously in the literature. It requires the structures of PBA to be surrounded by <i>n</i> explicit water molecules (PBA-W<span>\\(_n\\)</span>). The results show that the B(OH)<span>\\(_2\\)</span> unit of phenylboronic acid forms clusters with water molecules that are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenylboronic acid-water clusters are stabilized by strong OH<span>\\(\\cdots \\)</span>O and weak CH<span>\\(\\cdots \\)</span>O hydrogen bonds. In addition to QTAIM analysis, NBO analysis was also performed on the most stable configurations to better understand the delocalization of electron density from donor to proper acceptor within the compound. In addition, we found that the most stable structures dominate the population of the clusters for temperatures from 20 to 400 K. Finally, using the structures of the microhydrated phenylboronic acid, we estimated the free energy of hydration and the enthalpy of hydration of PBA. At room temperature, the phenylboronic acid’s free energy and enthalpy of hydration are respectively evaluated to be <span>\\(-\\)</span>72.1 kcal/mol and <span>\\(-\\)</span>85.5k cal/mol. Assessment of temperature effects on the free energy and the enthalpy of hydration shows that the enthalpy is temperature-independent, while the free energy increases linearly with temperature.</p><h3>\n <b>Methods</b>\n </h3><p>Initial configurations of PBA-W<span>\\(_n\\)</span> have been generated using classical molecular dynamics and subsequently optimized using the level of theory, <span>\\(\\omega \\)</span>B97X-D/def2-TZVP. Optimizations, frequency calculations, and NBO analysis are performed using the Gaussian 16 suite of programs. On the most stable configurations, we have performed the quantum theory of atoms in molecules (QTAIM) analysis to get insights into the hydrogen bond network of PBA-W<span>\\(_n\\)</span>. QTAIM is performed using AIMAll software. Thermodynamic properties as a function of temperature are evaluated using a homemade FORTRAN code-named <b>TEMPO</b>.</p></div>","PeriodicalId":651,"journal":{"name":"Journal of Molecular Modeling","volume":"31 8","pages":""},"PeriodicalIF":2.5000,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276122/pdf/","citationCount":"0","resultStr":"{\"title\":\"Microhydration of phenylboronic acid and its hydration free energy\",\"authors\":\"Doungous Sale, Alhadji Malloum, Mama Nsangou, Jean Jules Fifen, Jeanet Conradie\",\"doi\":\"10.1007/s00894-025-06436-2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>\\n <b>Context</b>\\n </h3><p>Understanding the interactions of phenylboronic acid with its surrounding water molecules is essential for several applications in solvated systems. In the present work, we investigated the microhydration of the phenylboronic acid (PBA) and calculated its hydration free energy using the cluster continuum solvation model. Microhydration of PBA has not been investigated previously in the literature. It requires the structures of PBA to be surrounded by <i>n</i> explicit water molecules (PBA-W<span>\\\\(_n\\\\)</span>). The results show that the B(OH)<span>\\\\(_2\\\\)</span> unit of phenylboronic acid forms clusters with water molecules that are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenylboronic acid-water clusters are stabilized by strong OH<span>\\\\(\\\\cdots \\\\)</span>O and weak CH<span>\\\\(\\\\cdots \\\\)</span>O hydrogen bonds. In addition to QTAIM analysis, NBO analysis was also performed on the most stable configurations to better understand the delocalization of electron density from donor to proper acceptor within the compound. In addition, we found that the most stable structures dominate the population of the clusters for temperatures from 20 to 400 K. Finally, using the structures of the microhydrated phenylboronic acid, we estimated the free energy of hydration and the enthalpy of hydration of PBA. At room temperature, the phenylboronic acid’s free energy and enthalpy of hydration are respectively evaluated to be <span>\\\\(-\\\\)</span>72.1 kcal/mol and <span>\\\\(-\\\\)</span>85.5k cal/mol. Assessment of temperature effects on the free energy and the enthalpy of hydration shows that the enthalpy is temperature-independent, while the free energy increases linearly with temperature.</p><h3>\\n <b>Methods</b>\\n </h3><p>Initial configurations of PBA-W<span>\\\\(_n\\\\)</span> have been generated using classical molecular dynamics and subsequently optimized using the level of theory, <span>\\\\(\\\\omega \\\\)</span>B97X-D/def2-TZVP. Optimizations, frequency calculations, and NBO analysis are performed using the Gaussian 16 suite of programs. On the most stable configurations, we have performed the quantum theory of atoms in molecules (QTAIM) analysis to get insights into the hydrogen bond network of PBA-W<span>\\\\(_n\\\\)</span>. QTAIM is performed using AIMAll software. Thermodynamic properties as a function of temperature are evaluated using a homemade FORTRAN code-named <b>TEMPO</b>.</p></div>\",\"PeriodicalId\":651,\"journal\":{\"name\":\"Journal of Molecular Modeling\",\"volume\":\"31 8\",\"pages\":\"\"},\"PeriodicalIF\":2.5000,\"publicationDate\":\"2025-07-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276122/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Molecular Modeling\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1007/s00894-025-06436-2\",\"RegionNum\":4,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q4\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Molecular Modeling","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s00894-025-06436-2","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Microhydration of phenylboronic acid and its hydration free energy
Context
Understanding the interactions of phenylboronic acid with its surrounding water molecules is essential for several applications in solvated systems. In the present work, we investigated the microhydration of the phenylboronic acid (PBA) and calculated its hydration free energy using the cluster continuum solvation model. Microhydration of PBA has not been investigated previously in the literature. It requires the structures of PBA to be surrounded by n explicit water molecules (PBA-W\(_n\)). The results show that the B(OH)\(_2\) unit of phenylboronic acid forms clusters with water molecules that are similar to those of neutral water clusters. The QTAIM analysis shows that the structures of phenylboronic acid-water clusters are stabilized by strong OH\(\cdots \)O and weak CH\(\cdots \)O hydrogen bonds. In addition to QTAIM analysis, NBO analysis was also performed on the most stable configurations to better understand the delocalization of electron density from donor to proper acceptor within the compound. In addition, we found that the most stable structures dominate the population of the clusters for temperatures from 20 to 400 K. Finally, using the structures of the microhydrated phenylboronic acid, we estimated the free energy of hydration and the enthalpy of hydration of PBA. At room temperature, the phenylboronic acid’s free energy and enthalpy of hydration are respectively evaluated to be \(-\)72.1 kcal/mol and \(-\)85.5k cal/mol. Assessment of temperature effects on the free energy and the enthalpy of hydration shows that the enthalpy is temperature-independent, while the free energy increases linearly with temperature.
Methods
Initial configurations of PBA-W\(_n\) have been generated using classical molecular dynamics and subsequently optimized using the level of theory, \(\omega \)B97X-D/def2-TZVP. Optimizations, frequency calculations, and NBO analysis are performed using the Gaussian 16 suite of programs. On the most stable configurations, we have performed the quantum theory of atoms in molecules (QTAIM) analysis to get insights into the hydrogen bond network of PBA-W\(_n\). QTAIM is performed using AIMAll software. Thermodynamic properties as a function of temperature are evaluated using a homemade FORTRAN code-named TEMPO.
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.