Solvation Model Research Articles

Experimental and computational studies on possibility of using glucose diazacrown cryptand as a carrier for anticancer drugs busulfan and lomustine

AbstractDrug carriers play a very important role in pharmacy, especially in cancer therapy. Most drugs used in the treatment of cancer are characterized by poor solubility in water and lack of selectivity in their toxic effects on normal and cancer cells. Administration of the drug in the form of a complex with an appropriately selected carrier can significantly improve its therapeutic effect and reduce side effects. In this study, the possibility of using the cryptand L1, containing two diazacrown ethers and two saccharide groups, as a potential drug carrier is investigated. In order to determine whether it can form complexes with drugs, the cryptand L1 and its complexes with two anticancer drugs, busulfan (BSF) and lomustine (CCNU), were synthesized. Their selected structural and energetic properties were investigated using both experimental and computational methods. Additionally, water solubility and cytotoxicity tests were performed for all compounds. The measured 1H NMR spectra confirm that L1 forms complexes L1:BSF and L1:CCNU, the solubility of which in water appears to be much higher than that of the pure drugs. The results of DFT calculations made in water described with the implicit solvent model confirm high stability of L1:BSF and L1:CCNU and indicate that L1 forms with the drugs mainly non-inclusion complexes. However, additional tests with 20 H2O molecules explicitly included in the model suggest that both inclusion and non-inclusion forms can occur in a real solution. Cytotoxicity studies show that the macrocycle L1 is non-toxic towards both normal and cancer cells, and its complexes with drugs show greater selectivity towards cancer cells. Interestingly, while the cytotoxicity of the L1:BSF complex is stronger than that of pure BSF, the relationship is opposite in the case of L1:CCNU and CCNU. Therefore, L1 can be considered as a potential drug carrier, especially for those drugs that have weak activity on cancer cells.

Development of Multiscale Force Field for Actinide (An3+) Solutions.

A multiscale force field (FF) is developed for an aqueous solution of trivalent actinide cations An3+ (An = U, Np, Pu, Am, Cm, Bk, and Cf) by using a 12-6-4 Lennard-Jones type potential considering ion-induced dipole interaction. Potential parameters are rigorously and automatically optimized by the meta-multilinear interpolation parametrization (meta-MIP) algorithm via matching the experimental properties, including ion-oxygen distance (IOD) and coordination number (CN) in the first solvation shell and hydration free energy (HFE). The water solvent models incorporate an especially developed polar coarse-grained (CG) water scheme named PW32 and three widely used all-atom (AA) level SPC/E, TIP3P, and TIP4P water schemes. Each PW32 is modeled as two bonded beads to represent three neighboring water molecules, the simulation efficiency of which is 1 to 2 orders of magnitude higher than that of AA waters. The newly developed FF shows high accuracy and transferability in reproducing the IOD, CN, and HFE of An3+. The molecular structure and water exchange dynamics of the first An3+ hydration shell and the ionic (van der Waals) radii are reinvestigated in this work. Moreover, the new FF can readily be transferred to other popular FFs, as it has practicably predicted the permeability of An3+ in a graphene oxide filter within the framework of optimized potentials for liquid simulations (OPLS)-AA FF. It holds promise for applications in exploring actinide aqueous solutions with multiscale computational overhead.

A Comparison of Modern Solvation Models for Oxygen Reduction at the Pt(111) Interface

A Comparison of Modern Solvation Models for Oxygen Reduction at the Pt(111) Interface

Fully Polarizable Multiconfigurational Self-Consistent Field/Fluctuating Charges Approach.

A multiscale model based on the coupling of the multiconfigurational self-consistent field (MCSCF) method and the classical atomistic polarizable fluctuating charges (FQ) force field is presented. The resulting MCSCF/FQ approach is validated by exploiting the CASSCF scheme through application to compute vertical excitation energies of formaldehyde and para-nitroaniline in aqueous solution. The procedure is integrated with molecular dynamics simulations to capture the solute's conformational changes and the dynamic aspects of solvation. Comparative analysis with alternative solvent models, gas-phase calculations, and experimental data provides insights into the model's accuracy in reproducing solute-solvent molecular interactions and spectral signals.

Spectroscopic, quantum computational, molecular dynamic simulations, and molecular docking investigation of the biologically important compound-2,6-diaminopyridine

To establish the role in future drug development, 2,6-diamino pyridine (2,6-DAP) was investigated experimentally using computational tools. NMR (1H,13C), FTIR, and UV–Vis spectra were analyzed for the titled compound. The molecular structure was optimized via DFT with the “B3LYP method with 6-311++G(d,p)” The optimized parameters of the structure were assessed with the observed bond characteristics. The vibrational frequencies were studied, PED was carried out, and the calculated vibrational frequency obtained was compared with the experimentally obtained FTIR. NMR (1H,13C) was calculated and compared with the experimentally obtained spectra. UV–vis spectra are calculated in the gaseous phase and different mediums of solvents (methanol, DMSO) by employing the PCM solvent model and TD-DFT method, and the estimated value was compared with experimentally measured data. NBO analysis was done to study the donor-acceptor interaction. The extent of electron charge transfer inside the molecular structure was examined using HOMO–LUMO energy values. The study of excitation analysis led to the creation of E.D.D and H.D.D maps in methanol and DMSO. The AIM and ELF analysis was employed to compute the iso-surface projections, ellipticity, and binding energies. The MEP and Fukui functions evaluate the molecule’s reactive zones. Hirshfeld research was done to analyze interactions among the molecules in the structure of the crystal, and 3D Hirshfeld tops and 2D fingerprint layouts were developed. The molecular docking procedure was used, followed by a 100 ns MD simulation and computation of binding free energy found to delineate the binding affinity of the molecule toward human carbonic anhydrase II (HCA II). Molecular docking studies with several receptor proteins were also conducted to determine the most effective protein-ligand interactions. Biological assessments like drug-likeness also act upon the compound to verify the molecule’s drug-like nature.

Application of the Linear Interaction Energy Method to Nitric Oxide Synthase Structure-Based Inhibitor Design.

The overproduction of nitric oxide by neuronal nitric oxide synthase (nNOS) is associated with several neuropathological conditions. As a result, inhibition of nNOS is a desirable therapeutic goal while avoiding the inhibition of endothelial NOS (eNOS) given its essential role in maintaining cardiovascular tone. Designing inhibitors with high specificity for nNOS over eNOS is challenging given the close similarity in the active site structure of all mammalian NOS isoforms. Computational methods like free energy perturbation (FEP) and thermodynamic integration (TI) offer attractive avenues for rational drug design, but application of these methods to NOS is hindered by several challenges, including proper handling of highly charged inhibitors with diverse structures as well as computational expense. To address these issues, we present a simplified approach combining continuum dielectric generalized born (GB) solvent models with linear interaction energy (LIE) calculations. Our method demonstrates excellent agreement with experimental data for charged inhibitors targeting mammalian NOS isoforms (mNOS). Our results highlight the utility of the GB-LIE method as a promising tool for screening NOS inhibitors and potentially other protein targets with charged active sites and diverse inhibitor structures.

Coarse-grained polarizable soft solvent models, with applications in dissipative particle dynamics.

We critically examine a broad class of explicitly polarizable soft solvent models aimed at applications in dissipative particle dynamics. We obtain the dielectric permittivity using the fluctuating box dipole method in linear response theory and verify the models in relation to several test cases, including demonstrating ion desorption from an oil-water interface due to image charge effects. We additionally compute the Kirkwood factor and find that it uniformly lies in the range gK≃0.7-0.8, indicating that dipole-dipole correlations are not negligible in these models. This is supported by the measurements of dipole-dipole correlation functions. As a consequence, Onsager theory over-predicts the dielectric permittivity by 20%-30%. The mean square molecular dipole moment can be accurately estimated with a first-order Wertheim perturbation theory.

Electric Field-Induced Sequential Prototropic Tautomerism in Enzyme-like Nanopocket Created by Single Molecular Break Junction.

Mastering the control of external stimuli-induced chemical transformations with detailed insights into the mechanistic pathway is the key for developing efficient synthetic strategies and designing functional molecular systems. Enzymes, the most potent biological catalysts, efficiently utilize their built-in electric field to catalyze and control complex chemical reactions within the active site. Herein, we have demonstrated the interfacial electric field-induced prototropic tautomerization reaction in acylhydrazone entities by creating an enzymatic-like nanopocket within the atomically sharp gold electrodes using a mechanically controlled break junction (MCBJ) technique. In addition to that, the molecular system used here contains two coupled acylhydrazone reaction centers, hence demonstrating a cooperative stepwise electric field-induced reaction realized at the single molecular level. Furthermore, the mechanistic studies revealed a proton relay-assisted tautomerization showing the importance of external factors such as solvent in such electric field-driven reactions. Finally, single-molecule charge transport and energetics calculations of different molecular species at various applied electric fields using a polarizable continuum solvent model confirm and support our experimental findings. Thus, this study demonstrates that mimicking an enzymatic pocket using a single molecular junction's interfacial electric field as a trigger for chemical reactions can open new avenues to the field of synthetic chemistry.

Discovery of the Most Stable Form of an Adenosine Receptor Antagonist through Virtual Polymorph Screening and Targeted Crystallization.

An innovative approach was developed to identify the optimal crystalline form, usually the thermodynamically most stable form. This method involves using virtual polymorph screening and targeted crystallization based on in silico solid-state modeling. By utilizing advanced crystal structure prediction (CSP) technology, the virtual polymorph screening method helps confirm whether the most stable crystalline form has been identified in actual crystallization experiments. If the predicted most stable form is not observed in experiments, predictions based on the method of COnductor like Screening MOdel for Real Solvents (COSMO-RS) are used to highlight solvent systems that can increase the likelihood of experimentally obtaining the desired form through a targeted crystallization process. In this work, such an approach has enabled the rapid discovery of the most stable polymorphic form and the development of a crystallization process of an adenosine receptor antagonist using minimal amounts of the sample within a shortened timeframe. Additionally, it provides a scientific rationale for ensuring the selection of the most stable form in the early stages of drug discovery, thereby reducing risks in future pharmaceutical development.

A "Turn-On" Fluorescent Probe for the Visual Detection of Total Iron in Wine.

A turn-on fluorescent sensor (E)-4-((4-(5-fluoro-1H-benzo[d]imidazol-2-yl)benzylidene)amino)phenol (FBAP) for the detection of Fe3+/2+ was synthesized. The fluorescence intensity of probe FBAP solution gradually increased with increased Fe3+ concentration. The low detection limit (LOD) was calculated to be 0.17 nM. The optimized structure and luminescent properties of FBAP were calculated by time-dependent density functional theory (TD-DFT) and Solvation Model Density (SMD). The rotation of the dihedral angle and ICT in the imine probe turned off the emission of the benzimidazole, which was restored upon cleaving the imine. Probe FBAP was successfully applied to determine whether Fe3+/2+ in wine exceeded the standard by phone and the rapid detection of Fe3+/2+ in the form of test strips was also conducted.

Multi-focal lipid membrane characterization by combination of DAS-deconvolution and anisotropy: Novel insight of fluorescence analysis

Three analogue solvatochromic probes, Laurdan, Prodan, and Acdan, are extensively used in the study of biological sciences. Their locations in lipid membranes vary greatly in depth, and their fluorescence responds to their surrounding environment based on their corresponding locations in the membrane. Utilizing the fluorescence lifetimes (τ) and emission peaks (λ) acquired from time-resolved emission spectrum, one can effectively determine the local lipid environment using the analytical approach refer to as τ and λ plots. Herein, τ and λ plot was created using the aforementioned probes to expand the analytical field according to their location. Furthermore, the solvent modeling method in τ and λ plot was upgraded to artificially emulate the complex environment in lipid membranes by utilizing liquid paraffin and glycerol to assess the contribution of viscosity to each fluorescence distribution. According to the results from a series of solvent mixtures, the effect of solvent viscosity on lifetime values was confirmed in the short lifetime region (∼ 3 ns). However, it was impossible to emulate the long lifetime values (4 ns ∼) observed in lipid membranes containing 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in the range of viscosity applied in this study. From the insight of the limiting anisotropy (r∞), the τ and λ plot was divided into a solvent-like region with isotropic environment (r∞ < 0.15) and a highly ordered region enough to define as anisotropic environment (0.15 <r∞) at τ: 4 ns. Also, the membrane-specific distribution was illustrated as 4 ns <τ and λ < 460 nm from this work. Updated analytical model was created to visualize multiple fluorescence components of each probe in 6 types of lipid bilayers, confirming the different distributions between these probes. Our results well-illustrated the multiplicity of lipid environments modeled with solvent and ordered environments in each lipid bilayer systems.

Phosphorylation of disordered proteins tunes local and global intramolecular interactions.

Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.

Prediction of Redox Potentials for Ac, Th, and Pa in Aqueous Solution.

Density functional theory in conjunction with small core pseudopotentials and the associated basis sets was used to calculate potentials for multiple redox couples, covering a range of oxidation states for Ac (0 to III), Th (0 to IV), and Pa (0 to V) in aqueous solution. Solvation effects were incorporated using a supermolecule-continuum approach, with 30 water molecules representing two solvation shells, and the COSMO and SMD implicit solvation models. The calculated geometries for Ac(III), Th(IV), and Pa(V) were in reasonable agreement with the available experimental data. Using the COSMO model with the B3LYP functional, the calculated redox potentials were within ±0.2 V from experiment for most redox couples. Several pathways were explored for the Pa(V/IV) redox couple for different forms of Pa(V) and Pa(IV). Most Pa(V/IV) redox couples have very similar potentials, ranging from 0 to -0.4 V up to a pH of 1.4. At pH = 1.4, the potentials shift to values that are more negative than -0.7 V, reflecting the growing unfavorable nature of the redox process at higher pH levels. The calculated values for An(III/II) potentials were consistent with prior estimates and the available experimental data. The predicted redox potentials for An(II/I) were highly negative, as expected. For An(I/0) potentials, Th and Pa exhibited positive values, contrasting with the negative values calculated for Ac. The An+m/An(0) potentials agreed better with the experimental data when using the COSMO solvation model as compared to the SMD model.

Predicting the solubility of CO2 and N2 in ionic liquids based on COSMO-RS and machine learning.

As ionic liquids (ILs) continue to be prepared, there is a growing need to develop theoretical methods for predicting the properties of ILs, such as gas solubility. In this work, different strategies were employed to obtain the solubility of CO2 and N2, where a conductor-like screening model for real solvents (COSMO-RS) was used as the basis. First, experimental data on the solubility of CO2 and N2 in ILs were collected. Then, the solubility of CO2 and N2 in ILs was predicted using COSMO-RS based on the structures of cations, anions, and gases. To further improve the performance of COSMO-RS, two options were used, i.e., the polynomial expression to correct the COSMO-RS results and the combination of COSMO-RS and machine learning algorithms (eXtreme Gradient Boosting, XGBoost) to develop a hybrid model. The results show that the COSMO-RS with correction can significantly improve the prediction of CO2 solubility, and the corresponding average absolute relative deviation (AARD) is decreased from 43.4% to 11.9%. In contrast, such an option cannot improve that of the N2 dataset. Instead, the results obtained from coupling machine learning algorithms with the COSMO-RS model agree well with the experimental results, with an AARD of 0.94% for the solubility of CO2 and an average absolute deviation (AAD) of 0.15% for the solubility of N2.

To Gibbs or Not to Gibbs Effect of Entropic Contribution in the NMR Calculations of Flexible and Polar Molecules-Updating the DP4+App.

The application of quantum-based NMR methods for the structural elucidation of natural and unnatural products has grown significantly. However, accurately calculating the conformational landscape of flexible molecules with intricate intramolecular hydrogen bonding (IHB) networks continues to be a major challenge. In this work, we thoroughly studied the effect of entropic contributions (trough Gibbs free energies calculations) in the DP4+ performance. Our results show that to solve biased systems with strong IHB interactions requires computing the Boltzmann contributions using Gibbs free energies computed with at least triple-ξ basis set and SMD solvation model. In response to this finding, we have updated our DP4+App, a user-friendly Python applet that automates the entire process of calculating DP4+ probabilities. In the new version, the program allows for calculating of conformational contributions at any selected theory level, using either SCF or Gibbs free energies.

Quantum mechanics/molecular mechanics (QM/MM) methods in drug design: a comprehensive review of development and applications

The integration of quantum mechanics (QM) and molecular mechanics (MM) methods, known as QM/MM, has emerged as a powerful computational approach in drug design. This hybrid technique combines the accuracy of QM calculations for the reactive region with the computational efficiency of MM methods for the surrounding environment. QM/MM methods have proven invaluable in studying chemical reactions, exploring enzyme mechanisms, and investigating ligand-protein interactions, all of which are crucial for rational drug design. This review provides a comprehensive overview of the QM/MM methodology, its theoretical foundations, and its applications in various aspects of drug design. We discussed the key components, such as QM and MM region partitioning, link atom schemes, and boundary treatments. Additionally, we highlight recent advancements and challenges in QM/MM methods, including polarizable force fields, implicit solvation models, and enhanced sampling techniques. Furthermore, we present illustrative examples showcasing the successful application of QM/MM methods in lead optimization, virtual screening, and the elucidation of biochemical mechanisms relevant to drug targets. Finally, we provide perspectives on future developments and the potential impact of QM/MM methods on the drug discovery pipeline.

Solvation modeling and optical properties of CdSO4-Doped L-Valine crystals

The utilization of computational solvation models for crystals proves effective in determining the amalgamation of molecular structures within the crystal medium, offering valuable insights into optimized crystal properties. This study focuses on identifying the arrangement of molecular strips within the crystal, crucial for recognizing active planes and the presence of non-linear optical (NLO) properties. To delve into the crystal's intricacies, a computational model was developed, and conformational analysis was conducted to ensure NLO property. The synthesis of the CdSO4-doped L-Valine metallo-organic complex crystal was achieved through the melt-freezing technique. The computational model was constructed to elucidate the formation of sub-planes within a confirmed orthorhombic crystal lattice. Mapping the molecular charge distribution with the dispersion of charge gradient facilitated the identification of chemical potential inhibition and its equipotential nodal domains. The estimation of electron density potential over critical points of the core carbons provided further insights. Chemical dynamics on the electron content of molecules for NLO properties were investigated by screening control parameters. The inelastic scattering ability of heteronuclear bonds for enhancing boosting potential was observed. Interactive frontier orbitals of degenerate energy states were illustrated, and the chemical potential of molecular zones was analyzed in-depth.

Superacid-Synthesized Fluorinated Diamines Act as Selective hCA IV Inhibitors.

Carbonic anhydrase (CA) IV is a membrane-bound enzyme involved in important physio-pathological processes, such as excitation-contraction coupling in heart muscle, central nervous system (CNS) extracellular buffering, and mediation of inflammatory response after stroke. Known since the mid-1980s, this isoform is still largely unexplored when compared to other isoforms, mostly for the current lack of inhibitors targeting selectively this isoform. The discovery of selective CA IV inhibitors is thus largely awaited. In this work, we report β-(di) fluoropropyl diamines as effective CA IV inhibitors, opening real perspectives for a new mode of selective inhibition of this isoform. Inhibition data reveal that the essential structure core to ensure a potent and selective inhibition of CA IV is the N-propyldiamine. Molecular modeling studies were employed to understand the binding mode of the synthesized amines. Conformational searches within the active site space carried out in an implicit solvent (water) model were also conducted.

Predicting hygroscopic growth of organosulfur aerosol particles using COSMOtherm

Abstract. Organosulfur (OS) compounds are important sulfur species in atmospheric aerosol particles, due to the reduction of global inorganic sulfur emissions. Understanding the physicochemical properties, such as hygroscopicity, of OS compounds is important for predicting future aerosol–cloud–climate interactions. However, their hygroscopicity is not yet well understood due to the scarcity of authentic standards. In this work, we investigated a group of OS compounds with short carbon chains (C1–C5) and oxygen-containing functional groups in the form of sodium, potassium, or ammonium salts and their mixtures with ammonium sulfate. The hygroscopic growth factors (HGFs) of these OS compounds have been experimentally studied. Here, the HGFs were calculated from mass fraction of water that was computed using the conductor-like screening model for real solvents (COSMO-RS). A good agreement was found between the model-estimated and experimental HGFs for the studied OS compounds. This quantum-chemistry-based approach for HGF estimation will open up the possibility of investigating the hygroscopicity of other OS compounds present in the atmosphere.

Improvement of tetracycline removal using amino acid ionic liquid modified magnetic biochar based on theoretical design

In current research, biochar is widely used to remove antibiotic contamination from the environment. However, original biochar produced through direct pyrolysis has significant limitations in removing antibiotics. In this paper, response surface methodology provided the laudable choice for magnetic poplar biochar (MPBC) considering the synergistic effect of multi-factors as well as the restrictions abundance experiments during the preparation of MPBC. Amino acid ionic liquids (AAILs) are a class of ionic liquids in which amino acids act as the anionic component, combining the tunable properties of ionic liquids with the biocompatibility and functionality of amino acids. To ameliorate adsorption capacity of MPBC, tetra-ethylammonium glycinate ([TEA][Gly]) with the best affinity for tetracycline (TC) were screened from 600 AAILs based on theoretical predictions using the conductor-like screening model for real solvents (COSMO-RS) without extensive experimental. Furthermore, AAILs-modified magnetic biochar (MPBC-AAIL) was synthesized chemically for the first time. Adsorption kinetics, isotherms, and thermodynamic analyses revealed that TC adsorption by both MPBC and MPBC-AAIL is a monolayer, spontaneous, and exothermic chemical process. Moreover, MPBC-AAIL exhibited a maximum adsorption capacity of 305.9 mg·g−1. Meanwhile, MPBC-AAIL maintains superior adsorption performance for TC in different impurity solutions as well as in real water samples. The excellent reusability and selective adsorption capacity of the material demonstrate the superiority of the theoretical based design. The characterization reveals that the adsorption mechanisms include pore filling, π-π interactions, surface complexation, hydrogen bonding, and electrostatic interactions. In addition, theoretical calculations showed that ionic liquid modification altered the adsorption sites between TC and MPBC-AAIL, leading to enhanced adsorption. This comprehensive study introduces an innovative modification of biochar, providing a novel approach to designing biochar composites and promoting their application in the remediation of complex environmental pollution.