Hydrophobicity of an isobutane dimer in water, methanol and acetonitrile as solvents — A classical molecular dynamics study

2019 ◽  
Vol 33 (32) ◽  
pp. 1950391
Author(s):  
Sailesh Bataju ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Center Of Mass ◽  
Sampling Technique ◽  
Md Simulations ◽  
Solvation Shell ◽  
Umbrella Sampling ◽  
Water Model ◽  
Solvent Environment ◽  
Potential Of Mean Forces

The potential of mean forces (PMFs) has been determined for an isobutane dimer in various solvent environments such as water, methanol and acetonitrile at a temperature of 298 K and pressure of 1 bar using GROMACS software. All the molecular dynamics (MD) simulations are carried out using a TIP3P water model under a CHARMM36 forcefield. Following Umbrella Sampling technique, PMFs are calculated and analyzed using Weighted Histogram Analysis Method (WHAM) and coordination number of first solvation shell is extracted for all solvents using radial distribution function. The shape of PMFs contains contact minima, solvent-separated minima and desolvation maxima. The values of contact minima are not affected much by solvent environment and found to be at 0.5377, 0.5480 and 0.5495 nm for water, methanol and acetonitrile respectively. The corresponding energy depths are found −0.9134, −0.7080 and −0.5295 kcalmol[Formula: see text]. The variation observed at solvent-separated minima is noticeable and found at 0.9012, 0.9721 and 0.9151 nm for water, methanol and acetonitrile, respectively. The coordination number of the first solvation shell by taking an isobutane molecule as a reference from their center of mass is found to be 28.1, 16.9 and 14.8 for water, methanol and acetonitrile, respectively. There is a soft hydrophobic interaction between isobutane dimer and solvents like methanol and acetonitrile relative to water, might be due to the presence of competitive methyl group of methanol and acetonitrile in the solvent medium.

scholarly journals Hydrophobicity of small alkane molecules (propane dimer) in solvents: a classical molecular dynamics study

BIBECHANA ◽  
2020 ◽  
Vol 17 ◽  
pp. 1-12
Author(s):  
Bikash Panthi ◽  
Nurapati Pantha
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Histogram Analysis ◽  
Analysis Method ◽  
Classical Molecular Dynamics ◽  
Solvent Environment ◽  
Weighted Histogram ◽  
Weighted Histogram Analysis

Molecular Dynamics (MD) simulations of propane dimer in different solvents (water, acetonitrile and methanol) were performed by using CHARMM platform for modeling the solute and solvents. A series of Umbrella sampling MD simulations were carried out in each solvent separately and potential of mean force (PMFs) were calculated by using Weighted Histogram Analysis Method. Results show that two minima (contact minima and solvent separated minima) characterize the PMF of propane dimer in all three solvent environments. The contact minima are deeper and less sensitive to solvent environment for its position. However, significant effect in the position of second minima, solvent separated minima, was observed. Our study reveals that the interaction between propane dimer is softer in methanol and acetonitrile than in water. BIBECHANA 17 (2020) 1-12  

scholarly journals Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

2017 ◽  
Author(s):  
Irfan Alibay ◽  
Kepa K. Burusco ◽  
Neil J. Bruce ◽  
Richard A. Bryce
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Biological Action ◽  
Sialyl Lewis X ◽  
Enhanced Sampling ◽  
Sialyl Lewis ◽  
Aqueous Solvent ◽  
A Minor

<p>Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 ms trajectories; these simulations find a predominance of closed conformer and a range of low occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the <sup>4</sup>C<sub>1</sub> form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution, corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.</p>

scholarly journals Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

2019 ◽  
Author(s):  
Joao Victor de Souza Cunha ◽  
Francesc Sabanes Zariquiey ◽  
Agnieszka K. Bronowska
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Water Model ◽  
High Plasticity ◽  
Solvation Model ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental and computational structural studies. To provide detailed atomic insight in IDPs dynamics governing its functional mechanisms, all-atom molecular dynamics (MD) simulations are widely employed. However, the current generalist force fields and solvent models are unable to generate satisfactory ensembles for IDPs when compared to existing experimental data. In this work, we present a new solvation model, denoted as Charge-Augmented 3 Point Water model for Intrinsically-disordered Proteins (CAIPi3P). CAIPi3P has been generated by performing a systematic scanning of atomic partial charges assigned to the widely popular molecular scaffold of the three-point TIP3P water model. We found that explicit solvent MD simulations employing CAIPi3P solvation considerably improved the SAXS scattering profiles for three different IDPs. Not surprisingly, this improvement was further enhanced by using CAIPi3P water in combination with the protein force field parametrized for IDPs. We have also demonstrated applicability of CAIPi3P to molecular systems containing structured as well as intrinsically disordered regions/domains. Our results highlight the crucial importance of solvent effects for generating molecular ensembles of IDPs which reproduce the experimental data available. Hence, we conclude that our newly developed CAIPi3P solvation model is a valuable tool assisting molecular simulations of intrinsically disordered proteins and assessing their molecular dynamics.

scholarly journals Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

2020 ◽  
Vol 21 (17) ◽  
pp. 6166
Author(s):  
Joao V. de Souza ◽  
Francesc Sabanés Zariquiey ◽  
Agnieszka K. Bronowska
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Water Model ◽  
High Plasticity ◽  
Solvation Model ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental and computational structural studies. To provide detailed atomic insight in IDPs’ dynamics governing their functional mechanisms, all-atom molecular dynamics (MD) simulations are widely employed. However, the current generalist force fields and solvent models are unable to generate satisfactory ensembles for IDPs when compared to existing experimental data. In this work, we present a new solvation model, denoted as the Charge-Augmented Three-Point Water Model for Intrinsically Disordered Proteins (CAIPi3P). CAIPi3P has been generated by performing a systematic scan of atomic partial charges assigned to the widely popular molecular scaffold of the three-point TIP3P water model. We found that explicit solvent MD simulations employing CAIPi3P solvation considerably improved the small-angle X-ray scattering (SAXS) scattering profiles for three different IDPs. Not surprisingly, this improvement was further enhanced by using CAIPi3P water in combination with the protein force field parametrized for IDPs. We also demonstrated the applicability of CAIPi3P to molecular systems containing structured as well as intrinsically disordered regions/domains. Our results highlight the crucial importance of solvent effects for generating molecular ensembles of IDPs which reproduce the experimental data available. Hence, we conclude that our newly developed CAIPi3P solvation model is a valuable tool for molecular simulations of intrinsically disordered proteins and assessing their molecular dynamics.

scholarly journals The transition mechanism of DNA overstretching: a microscopic view using molecular dynamics

2014 ◽  
Vol 11 (97) ◽  
pp. 20140399 ◽  
Author(s):  
L. Bongini ◽  
V. Lombardi ◽  
P. Bianco
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Average Distance ◽  
Sampling Technique ◽  
Energy Difference ◽  
Umbrella Sampling ◽  
Energy Profile ◽  
Structural Explanation ◽  
Free Energy Profile ◽  
Transition Mechanism

The overstretching transition in torsionally unconstrained DNA is studied by means of atomistic molecular dynamics simulations. The free-energy profile as a function of the length of the molecule is determined through the umbrella sampling technique providing both a thermodynamic and a structural characterization of the transition pathway. The zero-force free-energy profile is monotonic but, in accordance with recent experimental evidence, becomes two-state at high forces. A number of experimental results are satisfactorily predicted: (i) the entropic and enthalpic contributions to the free-energy difference between the basic (B) state and the extended (S) state; (ii) the longitudinal extension of the transition state and (iii) the enthalpic contribution to the transition barrier. A structural explanation of the experimental finding that overstretching is a cooperative reaction characterized by elementary units of approximately 22 base pairs is found in the average distance between adenine/thymine-rich regions along the molecule. The overstretched DNA adopts a highly dynamical and structurally disordered double-stranded conformation which is characterized by residual base pairing, formation of non-native intra-strand hydrogen bonds and effective hydrophobic screening of apolar regions.

scholarly journals Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

2019 ◽  
Author(s):  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Pengyu Ren
Keyword(s):  
Molecular Dynamics ◽  
Atomic Charge ◽  
Md Simulations ◽  
Water Model ◽  
Local Geometry ◽  
Important Ingredient ◽  
Binding Interaction ◽  
Molecular Systems ◽  
Water Models ◽  
Charge Flux

Molecular dynamics (MD) simulations employing classical force fields (FFs) have been widely used to model molecular systems. The important ingredient of the current FFs, atomic charge, remains fixed during MD simulations despite the atomic environment or local geometry changes. This approximation hinders the transferability of the potential being used in multiple phases. Here we implement a geometry dependent charge flux (GDCF) model into the multipole-based AMOEBA+ polarizable potential. The CF in the current work explicitly depends on the local geometry (<i>bond and angle</i>) of the molecule. To our knowledge, this is the first study that derives energy and force expressions due to GDCF in a multipole-based polarizable FF framework. Due to the inclusion of GDCF, the AMOEBA+ water model is noticeably improved in terms of describing the monomer properties, cluster binding/interaction energy and a variety of liquid properties, including the infrared spectra that previous flexible water models were not able to capture.

scholarly journals Structure and Dynamics of Curcumin Encapsulated Lecithin Micelles: A Molecular Dynamics Simulation Study

2021 ◽  
Vol 6 (3) ◽  
pp. 113-120
Author(s):  
Lukman Hakim ◽  
Diah Mardiana ◽  
Urnik Rokhiyah ◽  
Maria Lucia Ardhani Dwi Lestari ◽  
Zubaidah Ningsih
Keyword(s):  
Molecular Dynamics ◽  
Self Assembly ◽  
Local Density ◽  
Center Of Mass ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Spherical Micelle ◽  
Natural Surfactant ◽  
Dynamics Response ◽  
Nano Emulsion

Curcumin is a natural product with potential pharmaceutical applications that can be augmented by drug delivery technology such as nano emulsion. Our study focuses on microscopic structural and dynamics response of curcumin encapsulation in micellar system with lecithin as a natural surfactant under variations of composition and temperature using molecular dynamics (MD) simulations. The results highlight the self-assembly of lecithin micelle, with curcumin encapsulated inside, from initial random configurations in the absence of external field. The variation of composition shows that lecithin can aggregate into spherical and rod-like micelle with the second critical micelle concentration lies between 0.17-0.22 mol dm−3. The radial local density centering at the micelle center of mass shows that the effective radius of micelle is indeed defined by the hydrophilic groups of lecithin molecule and theencapsulated curcumin molecules are positioned closer to these hydrophilic groups than the innermost part of the micelle. The spherical micelle is shown to be thermally stable within the temperature range of 277-310 K without a perceivable change in the spherical eccentricity. The dynamics of micelle are enhanced by the temperature, but it is shown to be insensitive to the variation of lecithin-curcumin composition within the studied range. Simulation results are in agreement with the pattern obtained from experimental results based on particle size, polydispersity index, and encapsulation efficiency.

scholarly journals Surface Stability and Morphology of Calcium Phosphate Tuned by pH Values and Lactic Acid Additives: Theoretical and Experimental Study

2021 ◽  
Author(s):  
Hongwei Chen ◽  
Changchang Lv ◽  
Lin Guo ◽  
Ming Ma ◽  
Xiangfeng Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Lactic Acid ◽  
Calcium Phosphate ◽  
Coordination Number ◽  
Density Functional ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Surface Stability ◽  
Ph Values ◽  
Phosphate Species

The ubiquitous mineralization of calcium phosphate (CaP) facilitates biological organisms to produce hierarchically structured minerals. The coordination number and strength of Ca2+ ions with phosphate species, oxygen-containing additives, and solvent molecules played a crucial role in tuning nucleation processes and surface stability of CaP under the simulated body fluid (SBF) or aqueous solutions upon the addition of oligomeric lactic acid (LACn, n=1, 8) and changing pH values. As revealed by ab initio molecular dynamics (AIMD), density functional theory (DFT), and molecular dynamics (MD) simulations as well as high-throughput experimentation (HTE), the binding of LAC molecules with Ca2+ ions and phosphate species could stabilize both pre-nucleation clusters and brushite (DCPD, CaHPO4·2H2O) surface through intermolecular electrostatic and hydrogen bonding interactions. When the concentration of Ca2+ ions ([Ca2+]) is very low, the amount of the formed precipitation decreased with the addition of LAC based on UV-Vis spectroscopic analysis due to the reduced chance for the LAC capped Ca2+ ions to coordinate with phosphates and the increased solubility in acid solution. With the increasing [Ca2+] concentration, the kinetically stable DCPD precipitation was obtained with high Ca2+ coordination number and low surface energy. Morphologies of DCPD precipitation are in plate, needle, or rod, depending on the initial pH values that tuned by adding NH3·H2O, HCl, or CH3COOH. The prepared samples at pH ≈ 7.4 with different Ca/P ratios exhibited negative zeta potential values, which were correlated with the surface electrostatic potential distributions and potential biological applications.

scholarly journals MOLECULAR DYNAMICS STUDY OF OLEIC ACID-BASED SURFACTANTS FOR ENHANCED OIL RECOVERY

2020 ◽  
Vol 41 (3) ◽  
pp. 125-135
Author(s):  
Aang Suhendar ◽  
Rukman Hertadi ◽  
Yani F Alli
Keyword(s):  
Molecular Dynamics ◽  
Oleic Acid ◽  
Polyethylene Glycol ◽  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Md Simulation ◽  
Md Simulations ◽  
Water Model ◽  
Water Layers ◽  
Different Temperatures

Surfactants have been intensively used for Enhanced Oil Recovery (EOR). Nevertheless, environmental issues cause some surfactants to become unfavored in EOR application. Biodegradable surfactants are the suitable choice to make the environment safer. However, screening surfactants that have a good performance for EOR are time-consuming and costly. Molecular Dynamics (MD) simulation is an alternative solution to reduce cost and time. In the present study, oleic acid-based surfactants that combined with the various length of polyethylene glycol were studied. The potential surfactants were screened by MD simulation to evaluate their ability to reduce the Interfacial Tension (IFT) between oil and water layers, which is the by GROMACS software with Gromos force field and SPC water model. Carboxyl-terminal of the oleic acid was substituted by a different length of polyethylene glycol. All MD simulations were prepared in octadecanewater mixture with temperature ranges of 303-363 K. Our simulations found that the increasing number of polyethylene glycol was not always followed by the decreasing of IFT value between octadecane and water layers. These results were validated with the experimental data and found the similar IFT profile. The simulation of oil emulsification showed that all surfactant samples have good performance and stability as exhibited by their emulsification rate and emulsion stability in different temperatures. The last test to get the best surfactant was the wetability test. The simulation gave the result that both PEG100-oleic and PEG400-oleic were able to change wetability of rocks from oil-wet to water-wet. Accordingly, PEG400-oleic is the best nonionic surfactant candidate due to its performance in each simulation test.

scholarly journals Development of Charge-Augmented Three-Point Water Model (CAIPi3P) for Accurate Simulations of Intrinsically Disordered Proteins

2019 ◽  
Author(s):  
Joao Victor de Souza Cunha ◽  
Francesc Sabanes Zariquiey ◽  
Agnieszka K. Bronowska
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Md Simulations ◽  
Disordered Proteins ◽  
Water Model ◽  
High Plasticity ◽  
Solvation Model ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions

Intrinsically disordered proteins (IDPs) are molecules without a fixed tertiary structure, exerting crucial roles in cellular signalling, growth and molecular recognition events. Due to their high plasticity, IDPs are very challenging in experimental and computational structural studies. To provide detailed atomic insight in IDPs dynamics governing its functional mechanisms, all-atom molecular dynamics (MD) simulations are widely employed. However, the current generalist force fields and solvent models are unable to generate satisfactory ensembles for IDPs when compared to existing experimental data. In this work, we present a new solvation model, denoted as Charge-Augmented 3 Point Water model for Intrinsically-disordered Proteins (CAIPi3P). CAIPi3P has been generated by performing a systematic scanning of atomic partial charges assigned to the widely popular molecular scaffold of the three-point TIP3P water model. We found that explicit solvent MD simulations employing CAIPi3P solvation considerably improved the SAXS scattering profiles for three different IDPs. Not surprisingly, this improvement was further enhanced by using CAIPi3P water in combination with the protein force field parametrized for IDPs. We have also demonstrated applicability of CAIPi3P to molecular systems containing structured as well as intrinsically disordered regions/domains. Our results highlight the crucial importance of solvent effects for generating molecular ensembles of IDPs which reproduce the experimental data available. Hence, we conclude that our newly developed CAIPi3P solvation model is a valuable tool assisting molecular simulations of intrinsically disordered proteins and assessing their molecular dynamics.

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