TIP3P Water Model Research Articles

Monte Carlo simulations for free energies of hydration: Past to present.

A summary of the development of Monte Carlo statistical mechanics simulations for the computation of free energies of hydration of organic molecules is followed by presentation of results with the latest version of the optimized potentials for liquid simulations-all atom force field and the TIP4P water model. Scaling of the Lennard-Jones interactions between water, oxygen, and carbon atoms by a factor of 1.25 is found to improve the accuracy of free energies of hydration for 50 prototypical organic molecules from a mean unsigned error of 1.0-1.2 to 0.4 kcal/mol.

Formation of a two-dimensional helical square tube ice in hydrophobic nanoslit using the TIP5P water model.

In extreme and nanoconfinement conditions, the tetrahedral arrangement of water molecules is challenged, resulting in a rich and new phase behavior unseen in bulk phases. The unique phase behavior of water confined in hydrophobic nanoslits has been previously observed, such as the formation of a variety of two-dimensional (2D) ices below the freezing temperature. The primary identified 2D ice phase, termed square tube ice (STI), represents a unique arrangement of water molecules in 2D ice, which can be viewed as an array of 1D ice nanotubes stacked in the direction parallel to the confinement plane. In this study, we report the molecular dynamics (MD) simulations evidence of a novel 2D ice phase, namely, helical square tube ice (H-STI). H-STI is characterized by the stacking of helical ice nanotubes in the direction parallel to the confinement plane. Its structural specificity is evident in the presence of helical square ice nanotubes, a configuration unseen in both STI and single-walled ice nanotubes. A detailed analysis of the hydrogen bonding strength showed that H-STI is a 2D ice phase diverging from the Bernal-Fowler-Pauling ice rules by forming only two strong hydrogen bonds between adjacent molecules along its helical ice chain. This arrangement of strong hydrogen bonds along ice nanotube and weak bonds between the ice nanotube shows a similarity to quasi-one-dimensional van der Waals materials. Ab initio molecular dynamics simulations (over a 30ps) were employed to further verify H-STI's stability at 1GPa and temperature up to 200K.

Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes.

Glycosaminoglycans (GAGs) made of repeating disaccharide units intricately engage with proteins, playing a crucial role in the spatial organization of the extracellular matrix (ECM) and the transduction of biological signals in cells to modulate a number of biochemical processes. Exploring protein-GAG interactions reveals several challenges for their analysis, namely, the highly charged and periodic nature of GAGs, their multipose binding, and the abundance of the interfacial water molecules in the protein-GAG complexes. Most of the studies on protein-GAG interactions are conducted using the TIP3P water model, and there are no data on the effect of various water models on the results obtained in molecular dynamics (MD) simulations of protein-GAG complexes. Hence, it is essential to perform a systematic analysis of different water models in MD simulations for these systems. In this work, we aim to evaluate the properties of the protein-GAG complexes in MD simulations using different explicit: TIP3P, SPC/E, TIP4P, TIP4PEw, OPC, and TIP5P and implicit: IGB = 1, 2, 5, 7, and 8 water models to find out which of them are best suited to study the dynamics of protein-GAG complexes. The FF14SB and GLYCAM06 force fields were used for the proteins and GAGs, respectively. The interactions of several GAG types, such as heparin, chondroitin sulfate, and hyaluronic acid with basic fibroblast growth factor, cathepsin K, and CD44 receptor, respectively, are investigated. The observed variations in different descriptors used to study the binding in these complexes emphasize the relevance of the choice of water models for the MD simulation of these complexes.

Molecular Recognition of Moringa oleifera Active Compounds for Stunted Growth Prevention Using Network Pharmacology and Molecular Modeling Approach.

In this study, network pharmacology was used to analyze the active compounds of Moringa oleifera as food supplements for stunted growth prevention. Thirty-eight important proteins were discovered that may be strongly related to stunting. Those proteins were uploaded to several online tool platforms in order to determine the shared genes' pathways. Six pathways were identified that may be correlated with human growth. Furthermore, ligands for molecular docking analysis were retrieved from the top 5 active substances discovered through experimental investigation. In the meantime, the first-degree rank based on the protein-protein interaction (PPI) topological analysis was utilized to choose albumin protein (ALB) as a receptor. Our docking results showed that every ligand binds to the receptors, indicating that they can bind to the binding site of the ALB protein to form a complex formation. Further, MD simulation was used to verify the stability of the ligand in complex with the protein in the TIP3P water model. Based on the validation parameters, our results suggested that all models achieved a stable phase along the simulation. Additionally, the MM-GBSA method was used to calculate the binding energies of all models. Ligands 2 and 4 have strong binding to the binding pocket of ALB, followed by ligands 3, 5, and 2, suggesting that those ligands could be promising food supplements that can be utilized for the prevention of stunted growth in children.

Molecular dynamics calculations of the enthalpy of vaporization for different water models

Phase-change heat transfer processes involving water play a key role in numerous societal applications, such as electrical power generation, microelectronics cooling, or water desalination. Advanced computational tools, such as molecular dynamics (MD), are increasingly being used to simulate these processes, especially on nanostructured surfaces and in nanoparticle suspensions, to gain insight into the unique nanoscale physics at play. In these studies, it is critical to use models of the water molecule that yield accurate predictions of water’s thermophysical properties, particularly its enthalpy of vaporization. Here, we use MD to determine the enthalpy of vaporization (hfg) for six common water models and four different values of the cutoff radius (i.e., the intermolecular distance beyond which interactions are simplified or ignored). The most accurate prediction of hfg (within 2 % of the value tabulated by ASHRAE) comes from the TIP3P water model with a cutoff radius of 14 Å. We also conducted a preliminary study of the variation of hfg with pressure and found reasonable agreement between simulations and tabulated ASHRAE data (<7% error). This work provides physical insights into the sensitivity of the predicted macroscopic thermophysical properties of water to minute changes in the atomic-level properties and is expected to inform future MD-based studies of phase change processes of water, especially as they occur at elevated pressures and on nanostructured surfaces and in nanoconfined geometries.

Effect of Water Models on The Stability of RNA: Role of Counter-Ions

Various force fields and water model potentials influence significantly RNA conformations. The polyanionic nature of RNA attracts the water molecules and the counter ions which in turn affects their stability. The interfacial water's structural and dynamic aspects affect the RNA's base-pair opening and denaturation by breaking or making inter/intra-hydrogen bonds. Herein, we employed an MD simulations study using SPC/E and modified TIP3P water models in combination with different force fields CHARMM and AMBER to find their influence on the hydration shell of the SARS-CoV-2 RNA genome at different temperatures. AMBER-mTIP3P model was found to give more dynamic and transient conformations for RNA. The lower dielectric constant of the SPC/E model helps in the formation of the ion-contact pair near the negatively charged phosphate group (Na+-PO4−) leading to strong RNA-ion interaction and strong hydration shells having higher hydrogen bond lifetime. The Na+ ion survival probability at the interface was found to be more in the SPC/E model. At lower temperatures, the water molecules inside these hydration shells were found to be inhomogeneous, with lower void space, higher-coordinated, and non-tetrahedral. The higher dielectric constant of the mTIP3P model screened out the attraction between the ion pairs leading to a more homogenous solvation shell having a lesser hydrogen bond lifetime and more diffusive water. The distribution of the ions near the RNA structure is confirmed by metadynamics simulations. Both water models were found to disrupt the base pair orientation due to the formation of water bridges between the O2ʹ group of RNA and the water molecules.

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling.

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

Investigation of molecular details of a bacterial cationic amino acid transporter (GkApcT) during arginine transportation using molecular dynamics simulation and umbrella sampling techniques.

Cationic amino acid transporters (CATs) facilitate arginine transport across membranes and maintain its levels in various tissues and organs, but their overexpression has been associated with severe cancers. A recent study identified the alternating access mechanism and critical residues involved in arginine transportation in a cationic amino acid transporter from Geobacillus kaustophilus (GkApcT). Here, we used molecular dynamics (MD) simulation methods to investigate the transportation mechanism of arginine (Arg) through GkApcT. The results revealed that arginine strongly interacts with specific binding site residues (Thr43, Asp111, Glu115, Lys191, Phe231, Ile234, and Asp237). Based on the umbrella sampling, the main driving force for arginine transport is the polar interactions of the arginine with channel-lining residues. An in-depth description of the dissociation mechanism and binding energy analysis brings valuable insight into the interactions between arginine and transporter residues, facilitating the design of effective CAT inhibitors in cancer cells. The membrane-protein system was constructed by uploading the prokaryotic CAT (PDB ID: 6F34) to the CHARMM-GUI web server. Molecular dynamics simulations were done using the GROMACS package, version 5.1.4, with the CHARMM36 force field and TIP3P water model. The MM-PBSA approach was performed for determining the arginine binding free energy. Furthermore, the hotspot residues were identified through per-residue decomposition analysis. The characteristics of the channel such as bottleneck radius and channel length were analyzed using the CaverWeb 1.1 web server. The proton wire inside the transporter was investigated based on the classic Grotthuss mechanism. We also investigated the atomistic details of arginine transportation using the path-based free energy umbrella sampling technique (US).

Morse potential parameters of dissipative particle dynamics force fields for non-polarizable water models

The Morse potential parameters compatible with dissipative particle dynamics (DPD) for water are determined by the Ornstein-Zernike (OZ) equation with the hyper-netted chain (HNC) closure. The present study verifies that the HNC approximation is accurate for a DPD system described by the soft repulsive and Morse potentials. Firstly, we demonstrate that the modified form of the Morse potential is necessary for the numerical solution of the OZ/HNC equations. Subsequently, the Morse potential parameters for mimicking SPCE, TIP3P, TIP4P, and TIP5P water models within the DPD framework are determined by mapping the radial distribution function (RDF) in the HNC approximation to those of all-atom simulations. The first-peak positions and heights of the center-of-mass RDFs for all-atom water models are successfully reproduced by DPD simulations using the determined parameters. The OZ/HNC results for the RDFs and pressures, calculated for the obtained water models, are in satisfactory agreement with the DPD results. Moreover, we investigate how the addition of the Morse potential term to the solute-solvent interaction manifests itself in the solution properties. Major effects of the Morse potential are found in the solute-solvent RDF and the potential of mean force (PMF) between a pair of solutes. We discuss the molecular mechanism underlying the effects induced by the Morse potential in detail.

Effect of coarse graining in water models for the study of kinetics and mechanisms of clathrate hydrates nucleation and growth.

Clathrate hydrates are crystalline inclusion compounds wherein a water framework encages small guest atoms/molecules within its cavities. Among the others, methane clathrates are the largest fossil fuel resource still available. They can also be used to safely transport gases and can also form spontaneously under suitable conditions plugging pipelines. Understanding the crystallization mechanism is very important, and given the impossibility of experimentally identifying the atomistic path, simulations played an important role in this field. Given the large computational cost of these simulations, in addition to all-atom force fields, scientists considered coarse-grained water models. Here, we have investigated the effect of coarse-graining, as implemented in the water model mW, on the crystallization characteristics of methane clathrate in comparison with the all-atom TIP4P force field. Our analyses revealed that although the characteristics directly depending on the energetics of the water models are well reproduced, dynamical properties are off by the orders of magnitude. Being crystallization a non-equilibrium process, the altered kinetics of the process results in different characteristics of crystalline nuclei. Both TIP4P and mW water models produce methane clathrate nuclei with some amount of the less stable (in the given thermodynamic conditions) structure II phase and an excess of pentagonal dodecahedral cages over the tetrakaidecahedral ones regarding the ideal ratio in structure I. However, the dependence of this excess on the methane concentration in solution is higher with the former water model, whereas with the latter, the methane concentration in solution dependence is reduced and within the statistical error.

Implementation of solvation free energy framework to predict the vapor-liquid equilibrium behaviors for the water–hydrazine and ethanol–water azeotropic systems

An azeotrope is a special vapor–liquid equilibrium in which the composition of two coexisting phases is equal. Due to its strong deviation from the Raoult’s law, it poses a great challenge to the simple distillation process and the understanding of fundamental molecular mechanisms. In this study, we calculated the coupling work of solute species based on the solvation free energy framework to predict the vapor–liquid equilibrium (VLE) behavior and azeotrope point of mixtures. Two prototypical binary mixtures: the negative water-hydrazine and positive ethanol–water azeotrope were investigated using molecular dynamic simulations and the OPLS-AA force field. All the simulations were performed with the TIP3P water model, because it has a good capability to represent enthalpy properties. The molecular models of hydrazine and ethanol have been re-parameterized to reproduce the density and solvation free energy properties of pure substance. Using free energy perturbation simulation, the coupling work of each substance was studied against liquid mixture composition. The coupling work is also translated to x-y or T-x-y phase diagrams for comparison with available experimental data. The tendency of two azeotropes is that the more volatile components experience the less pronounced coupling work changes in their local environments as the azeotropes form. The coupling work is also divided into van der Waals and Coulomb contributions to investigate the interactions between particles. Lithium Chloride was investigated as an entrainer for the separation of ethanol–water system. The coupling works of binary mixtures were calculated at different salt concentrations to study the salt-out effect for the violate species and salt-in effect for the less violate species. By adding LiCl, it was found that the azeotrope point was efficiently eliminated at a salinity 0.05 mol fraction at 1 bar. All the results show that the simulation methodology of coupling work are reliable for calculating the liquid–vapor equilibrium behavior. This method is also valuable for selecting and designing new extractants for distillation process.

Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.

In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.

Extending the applicability of popular force fields for describing water/metal interfaces: application to water/Pd(111)

We propose a new method for constructing a polarizable classical force field using data obtained from QM and QM/MM calculations to account for the charge redistribution at the water/metal interface. The induced charge effects are described by adding dipoles to the system topology following the Rod Model (Iori, F, et al J. Comput. Chem.2009, 30, 1465). Furthermore, the force field uses the TIP3P water model, and its functional form is compatible with popular force fields such as AMBER, CHARMM, GROMOS, OPLS-AA, CVFF and IFF. The proposed model was evaluated and validated for water/Pd(111) systems. We tuned the model parameters to reproduce a few critical water/Pd(111) geometries and energies obtained from DFT calculations using both PBE and a non-local van der Waals xc-functional. Our model can reproduce the hexagonal ice layer for the Pd(111)/water systems typically present in low-temperature experiments, in agreement with information available from the literature. Additionally, the model can also reproduce the experimental metal-water interfacial tension at room temperature.

Enhanced thermophysical properties of water-based single and hybrid metallic nanofluids: Insights from Equilibrium Molecular Dynamics

The effect of single (Cu or Ag) and hybrid (Cu+Ag) metallic nanoparticles on the thermophysical properties, namely viscosity and thermal conductivity of water-based nanofluids, has been studied using Equilibrium Molecular dynamics (EMD) simulation. The TIP3P (three-site transferrable intermolecular potential) water model has been chosen. The interaction of water molecules has been modelled by the Lennard-Jones (L J) potential in combination with Coulomb potential. The embedded-atom (EAM) potential method has been used for hybrid (Cu and Ag) atom interaction. Simulation has been performed at 303 K and atmospheric pressure using the Berendsen algorithm under NVT (constant number, constant volume, and constant temperature) ensemble with production steps of 2 ns and integral step of 1fs. Interestingly, nanofluids containing one metallic nanoparticle (Cu or Ag) have lower thermal conductivity and viscosity than nanofluids having hybrid metallic nanoparticles with the same volume fraction.

Extraction of Dielectric Permittivity from Atomistic Molecular Dynamics Simulations and Microwave Measurements.

The design of new biotechnology depends on the prediction and measurement of the electrical properties of biomolecules. The dielectric permittivity, in particular, is highly important for the design of microwave systems for diagnostics, yet this property is rarely explicitly targeted during the development of biomolecular force fields for molecular dynamics (MD) simulations. In order to explore the ability of existing force fields to reproduce the frequency-dependent permittivity, we carried out MD simulations of various aqueous solutions, including pure water, isopropyl alcohol, alanine, and the protein ubiquitin. The TIP3P, TIP4P, TIP4P/ε, and SWM4-NDP water models were used along with the CHARMM36m and Drude protein force fields. An experimental setup using a truncated coaxial line was created to measure the permittivity of the same solutions to check for measure-model agreement. We found that one of the nonpolarizable force fields (TIP4P/ε + CHARMM36m) and the polarizable force fields (SWM4-NDP + Drude) closely agree with experimental results. This demonstrates the strength of the tuned TIP4P/ε water model, as well as the physical validity of polarizable force fields in capturing dielectric permittivity. This represents an important step toward the predictive design of biosensors.

The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes.

Modeling approaches and modern simulations to investigate the biomolecular structure and function rely on various methods. Since water molecules play a crucial role in all sorts of chemistry, the accurate modeling of water molecules is vital for such simulations. In cytochrome P450 (CYP450), in particular, water molecules play a key role in forming active oxidant that ultimately performs oxidation and metabolism. In the present study, we have highlighted the behavior of the three most widely used water models─TIP3P, SPC/E, and OPC─for three different CYP450 enzymes─CYP450BM3, CYP450OleT, and CYP450BSβ─during MD simulations and QM/MM calculations. We studied the various properties, such as RMSD, RMSF, H-bond, water occupancy, and hydrogen atom transfer (HAT), using QM/MM calculations and compared them for all three water models. Our study shows that the stabilities of the enzyme complexes are well maintained in all three water models. However, the OPC water model performs well for the polar active sites, that is, in CYP450OleT and CYP450BSβ, while the TIP3P water model is superior for the hydrophobic site, such as CYP450BM3.

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions.

Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs). The overestimation of protein-protein interactions tends to make IDPs more compact than those in experiments. Likewise, multiple proteins in crowded solutions are aggregated with each other too strongly. To optimize the balance, Lennard-Jones (LJ) interactions between protein and water are often increased about 10% (with a scaling parameter, λ = 1.1) from the existing force fields. Here, we explore the optimal scaling parameter of protein-water LJ interactions for CHARMM36m in conjunction with the modified TIP3P water model, by performing enhanced sampling MD simulations of several peptides in dilute solutions and conventional MD simulations of globular proteins in dilute and crowded solutions. In our simulations, 10% increase of protein-water LJ interaction for the CHARMM36m cannot maintain stability of a small helical peptide, (AAQAA)3 in a dilute solution and only a small modification of protein-water LJ interaction up to the 3% increase (λ = 1.03) is allowed. The modified protein-water interactions are applicable to other peptides and globular proteins in dilute solutions without changing thermodynamic properties from the original CHARMM36m. However, it has a great impact on the diffusive properties of proteins in crowded solutions, avoiding the formation of too sticky protein-protein interactions.

Dynamics of Topology-dependent Water Purification by Siliceous Zeolite Membranes

• Simulated the effect of topology and pore size of zeolites on water purification. • Compared porous LTA, FAU, and MFI zeolites in purification of Cl - , Pb 2+ , and Co 2+ . • Tersoff and Lennard-Jones hybrid force fields, and TIP3P water models were used. • Applying PMF in MD simulation, the efficiency of zeolite membranes was conceptualized. • Applying a long time of 15 ns, heavy metal ions behaved differently in rejection. The efficiency of pollutant rejection (PR, %) and water purification of the zeolite membranes is highly dependent on their topology, i.e., porosity and chemical composition. Nevertheless, mechanisms controlling such a physicochemical phenomenon have been limitedly discussed. Herein, we provide insights into the physics and dynamics of water purification by zeolite nanosheets in terms of topological variables. The molecular dynamics (MD) simulation pictured the molecular-lever water purification having heavy metal ions (Co 2+ and Pb 2+ ) as typical water contaminants. Three siliceous zeolites having different topologies, i.e., LTA, FAU, and MFI zeolites, were positioned in the simulation space. MD simulation was served under pressure and temperature of 24 MPa and 300 K, respectively, applying the Canonical ensemble (NVT) condition. The intermolecular interactions between contaminant ions, zeolite, and graphene were tracked by hybridizing Tersoff and Lenard-Jones potentials, while the TIP3P model of the CHARMM force field was used to simulate water dynamics. The LAMMPS software and Visual Molecular Dynamics (VMD) were used to collect data and graphics over 15 ns, with early 5 ns devoted to reaching equilibrium. Interestingly, we demonstrated by the aid of potential of the mean force (PMF) pollutant ions which encounter the zeolite pores smaller than their kinetic diameter consume more energy for permeation across the membrane, -reason why LTA appeared selective against Pb 2+ , Co 2+ , and Cl - ions, with PR of 40, 60, and 100%, respectively. The absolute water flux values were monitored, and LTA and FAU fluxes were ∼ 50% higher than MFI zeolite, but 5 ns after equilibrium, LTA flux was overtaken sharply by the simulation because of the larger pore size. Overall, the electrostatic forces showed absolute control over the purification but were governed by the zeolite topology.

A Coupled EXAFS-Molecular Dynamics Study on PuO2+ and NpO2+ Hydration: The Importance of Electron Correlation in Force-Field Building.

The physicochemical properties of the monovalent actinyl cations, PuO2+ and NpO2+, in water have been studied by means of classical molecular dynamic simulations. A specific set of cation-water intermolecular potentials based on ab initio potential energy surfaces has been built on the basis of the hydrated ion concept. The TIP4P water model was adopted. Given the paramagnetic character of these actinyls, the cation–water interaction energies were computed from highly correlated wave functions using the NEVPT2 method. It is shown that the multideterminantal character of the wave function has a relevant effect on the main distances of the hydrated molecular cations. Several structural, dynamical, and energetic properties of the aqueous solutions have been obtained and analyzed. Structural RDF analysis gives An–Oyl distances of 1.82 and 1.84 Å and An–O(water) distances of 2.51 and 2.53 Å for PuO2+ and NpO2+ in water, respectively. Experimental EXAFS spectra from dilute aqueous solutions of PuO2+ and NpO2+ are revisited and analyzed, assuming tetra- and pentahydration of the actinyl cations. Simulated EXAFS spectra have been computed from the snapshots of the MD simulations. Good agreement with the experimental information available is found. The global analysis leads us to conclude that both PuO2+ and NpO2+ cations in water are stable pentahydrated aqua ions.

Parameterization and Application of the General Amber Force Field to Model Fluoro Substituted Furanose Moieties and Nucleosides.

Molecular mechanics force field calculations have historically shown significant limitations in modeling the energetic and conformational interconversions of highly substituted furanose rings. This is primarily due to the gauche effect that is not easily captured using pairwise energy potentials. In this study, we present a refinement to the set of torsional parameters in the General Amber Force Field (gaff) used to calculate the potential energy of mono, di-, and gem-fluorinated nucleosides. The parameters were optimized to reproduce the pseudorotation phase angle and relative energies of a diverse set of mono- and difluoro substituted furanose ring systems using quantum mechanics umbrella sampling techniques available in the IpolQ engine in the Amber suite of programs. The parameters were developed to be internally consistent with the gaff force field and the TIP3P water model. The new set of angle and dihedral parameters and partial charges were validated by comparing the calculated phase angle probability to those obtained from experimental nuclear magnetic resonance experiments.