Sarupria group

Publications


2017

  1. On the water structure at hydrophobic interfaces and the roles of water on transition-metal catalyzed reactions: A short review
    Xiaohong Zhang, Torrie E. Sewell, Brittany Glatz, Sapna Sarupria, and Rachel B. Getman, Catalysis Today, 285, 57-64 (2017)
    [Abstract] [PDF]
    Interest into the roles of water on aqueous phase heterogeneous catalysis is burgeoning. This short review summarizes the influences of hydrogen bonding on adsorption and how water molecules act as co-catalysts in aqueous phase heterogeneous catalysis. These phenomena, which involve interactions and/or reactions with “dangling” hydroxyl or hydroxide groups from nearby water molecules, are related to interfacial phenomena that have been observed at water/oil interfaces in organic synthesis. The hypothesized water structures at water/oil interfaces in organic synthesis is presented, and predictions about how analogous structural effects could influence catalytic chemistry at water/transition metal interfaces are discussed. The focus of this review is on computational methods and observations, but some experimental methods and findings are discussed as well.
  2. A DFT and MD study of aqueous-phase dehydrogenation of glycerol on Pt(1 1 1): comparing chemical accuracy versus computational expense in different methods for calculating aqueous-phase system energies
    Tianjun Xie, Sapna Sarupria and Rachel B. Getman, Mol. Sim., 43, 370-378 (2017)
    [Abstract] [BibTeX] [PDF]
    Glycerol, which is one of the most abundant by-products in biodiesel production, can be converted into H2 through aqueous-phase reforming (APR). Dehydrogenation is one of the main processes in glycerol APR. In this work, we use computational methods to study Pt(1 1 1)-catalysed glycerol dehydrogenation under aqueous conditions. There are 84 intermediates and 250 possible reactions in the dehydrogenation network. Inclusion of the liquid environment adds computational expense, especially if we are to study all the reaction intermediates and reactions under explicit water solvation using quantum methods. In this work, we present a method that can be used to efficiently estimate reaction energies under explicit solvation with reasonable accuracy and computational expense. The method couples a linear scaling relationship for obtaining adsorbate binding energies with Lennard-Jones + Coulomb potentials for obtaining water–adsorbate interaction energies. Comparing reaction energies calculated with this approach to reaction energies obtained from a more extensive approach that attains quantum-level accuracy (published previously by our group), we find good correlation (R2 = 0.84) and reasonable accuracy (the mean absolute error, MAE = 0.28 eV).
    @Article{RBG:2017:MS,
    author = {Xie, T., Sarupria, S. and R. B. Getman} 
    title  = {{A DFT and MD study of aqueous-phase dehydrogenation of glycerol on Pt(1 1 1): comparing chemical accuracy versus computational expense in different methods for calculating aqueous-phase system energies }}
    journal  ={{Mol. Sim.}}
    year  ={2017},
    volume  = {},
    pages  = {1-9},
    doi  = {http://dx.doi.org/10.1080/08927022.2017.1285403},
    }
    

2016

  1. The surface charge distribution affects the ice nucleating efficiency of silver iodide
    Brittany Glatz and Sapna Sarupria, J. Chem. Phys., 145, 211924, (2016)
    [Abstract] [BibTeX] [PDF]
    Heterogeneous ice nucleation is the primary pathway for ice formation. However, the detailed molecular mechanisms by which surfaces promote or hinder ice nucleation are not well understood. We present results from extensive molecular dynamics simulations of ice nucleation near modified silver iodide (AgI) surfaces. The AgI surfaces are modified to investigate the effects of the surface charge distribution on the rate of ice nucleation. We find that the surface charge distribution has significant effects on ice nucleation. Specifically, AgI surfaces with the positive charges above the negative charges in the surface promote ice nucleation, while ice nucleation is hindered for surfaces in which the negative charges are above or in-plane with the positive charges. The structure of water molecules in the interfacial region as measured by the orientations of the water molecules relative to the surface can explain the differences in the ice nucleation at the different surfaces. We suggest that the distributions of the orientations of the interfacial water molecules could be used more broadly as a measure of ice nucleating propensity.
    @Article{Sarupria:2016:JCP,
    author = { Glatz, B. and Sarupria, S.} 
    title  = {{The surface charge distribution affects the ice nucleating efficiency of silver iodide}}
    journal  ={{J. Chem. Phys.}}
    year  ={2016},
    volume  = {145},
    pages  = {211924},
    doi  = {10.1063/1.4966018},
    }
    

2015

  1. Influence of carbon nanomaterial defects on the formation of protein corona
    Bishwambhar Sengupta, Wren E. Gregory, Jingyi Zhu, Siva Dasetty, Mehmet Karakaya, Jared M. Brown, Apparao M. Rao, John K. Barrows, Sapna Sarupria and Ramakrishna Podilla, RSc. Advances, 5, 82395-82402, (2015)
    [Abstract] [BibTeX] [PDF]
    In any physiological media, carbon nanomaterials (CNM) strongly interact with biomolecules leading to the formation of biocorona, which subsequently dictate the physiological response and the fate of CNMs. Defects in CNMs play an important role not only in material properties but also in the determination of how materials interact at the nano-bio interface. In this article, we probed the influence of defect-induced hydrophilicity on the biocorona formation using micro-Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge-transfer between them, inducing protein unfolding which enhances conformational entropy and higher protein adsorption.
    @Article{Podilla:2015:RScAdv,
    author = { Sengupta, B. and Gregory, W. E. and Zhu, J. and  Dasetty, S. and Karakaya, M. and  Brown, J. M. and  Rao, A. M. and Barrows, J. K. and Sarupria, S. and Podilla, R.}
    title  = {{Influence of carbon nanomaterial defects on the formation of protein corona}}
    journal  ={RSc. Adv.}
    year  ={2015},
    volume  = {5},
    pages  = {82395-82402},
    doi  = {10.1039/C5RA15007H},
    }
    
  2. Association of small aromatic molecules with PAMAM dendrimers
    Ryan S. DeFever and Sapna Sarupria, Phys. Chem. Chem. Phys., 17, 29548-29557, (2015)
    [Abstract] [BibTeX] [PDF]
    Many proposed applications using dendrimers, such as drug delivery and environmental re- mediation, involve dendrimer interactions with small molecules. Understanding the details of these interactions is important for designing dendrimers with tunable association with guest molecules. In this work, we investigate dendrimer interactions with small aromatic hydrocar- bons using all-atom molecular dynamics simulations. We study the association of naphthalene (NPH) — the smallest polycyclic aromatic hydrocarbon — with 3rd–6th generation (G3–G6) polyamidoamine (PAMAM) dendrimers. Our work emphasizes that the association of small aromatic molecules with PAMAM dendrimers involves the formation of dynamic pocket-like association sites through interactions between flexible dendrimer branches and NPH molecules. The association sites are primarily formed by branches from the two outermost dendrimer sub- generations, and often involve the tertiary amine groups. Irrespective of their location on the dendrimer — whether buried or near the outer surface — these pocket-like structures lower the hydration of the associated NPH molecules. We show that on average NPH molecules with a lower hydration have a greater tendency to remain associated with the dendrimer for longer times. In general, the association sites are similar for the G3–G6 PAMAM dendrimers indicating similarities in the association mechanisms across different dendrimer generations.
    @Article{RSD:2015:PCCP,
    author = {Ryan S. DeFever and Sapna Sarupria}
    title  = {{}}
    journal  ={Phys. Chem. Chem. Phys.}
    year  ={2015},
    volume  = {Just Accepted},
    pages  = {},
    doi  = {10.1039/C5CP03717D},
    }
    
  3. Molecular-Level Details about Liquid H2O Interactions with CO and Sugar Alcohol Adsorbates on Pt(111) Calculated Using Density Functional Theory and Molecular Dynamics
    Cameron J. Bodenschatz, Sapna Sarupria and Rachel Getman, J. Phys. Chem. C, 119, 13642-13651, (2015)
    [Abstract] [BibTeX] [PDF]
    Catalytic fuel production and energy generation from biomass-derived compounds generally involve the aqueous phase, and water molecules at the catalyst interface have energetic and entropic consequences on the reaction free energies. These effects are difficult to elucidate, hindering rational catalyst design for these processes and inhibiting their widespread adoption. In this work, we combine density functional theory (DFT) and classical molecular dynamics (MD) simulations to garner molecular-level insights into H2O–adsorbate interactions. We obtain ensembles of liquid configurations with classical MD and compute the electronic energies of these systems with DFT. We examine CO, CH2OH, and C3H7O3 intermediates, which are critical in biomass reforming and direct methanol electrooxidation, on the Pt(111) surface under various explicit and explicit/implicit water configurations. We find that liquid H2O molecules arrange around surface intermediates in ways that favor hydrogen bonding, with larger and more hydrophilic intermediates forming significantly more hydrogen bonds with H2O. For example, CO hydrogen-bonds with 1.5 ± 0.4 nearest neighbor H2O molecules and exhibits an interaction energy with these H2O molecules near 0 (−0.01 ± 0.09 eV), while CH2OH forms 2.2 ± 0.6 hydrogen bonds and exhibits an interaction energy of −0.43 ± 0.07 eV. C3H7O3 forms 6.7 ± 0.9 hydrogen bonds and exhibits an interaction energy of −1.18 ± 0.21 eV. The combined MD/DFT method identifies the number of liquid H2O molecules that are strongly bound to surface adsorbates, and we find that these H2O molecules influence the energies and entropies of the aqueous systems. This information will be useful in future calculations aimed at interrogating the surface thermodynamics and kinetics of reactions involving these adsorbates.
    @Article{Getman:2015:JPCC,
    author = {Cameron J. Bodenschatz, Sapna Sarupria and Rachel Getman},
    title  = {{Molecular-Level Details about Liquid H2O Interactions with CO and Sugar Alcohol Adsorbates on Pt(111) Calculated Using Density Functional Theory and Molecular Dynamics}}
    journal  ={J. Phys. Chem. C},
    year  ={2015},
    volume  = {119},
    pages  = {13642-13651},
    doi  = {10.1021/acs.jpcc.5b02333}
    }
    
  4. PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water
    Ryan S. DeFever, Nicholas K. Geitner, Priyanka Bhattacharya, Feng Ding, Pu Chun Ke, and Sapna Sarupria, Environ. Sci. Technol., 49, 4490-7, (2015)
    [Abstract] [BibTeX] [PDF]
    We present results from experiments and atomistic molecular dynamics simulations on the remediation of naphthalene by polyamidoamine (PAMAM) dendrimers and graphene oxide (GrO). Specifically, we investigate 3(rd)-6(th) generation (G3-G6) PAMAM dendrimers and GrO with different levels of oxidation. The work is motivated by the potential applications of these emerging nanomaterials in removing polycyclic aromatic hydrocarbon contaminants from water. Our experimental results indicate that GrO outperforms dendrimers in removing naphthalene from water. Molecular dynamics simulations suggest that the prominent factors driving naphthalene association to these seemingly disparate materials are similar. Interestingly, we find that cooperative interactions between the naphthalene molecules play a significant role in enhancing their association to the dendrimers and GrO. Our findings highlight that while selection of appropriate materials is important, the interactions between the contaminants themselves can also be important in governing the effectiveness of a given material. The combined use of experiments and molecular dynamics simulations allows us to comment on the possible factors resulting in better performance of GrO in removing polyaromatic contaminants from water. We present results from experiments and atomistic molecular dynamics simulations on the remediation of naphthalene by polyamidoamine (PAMAM) dendrimers and graphene oxide (GrO). Specifically, we investigate 3rd-6th generation (G3-G6) PAMAM dendrimers and GrO with different levels of oxidation. The work is motivated by the potential applications of these emerging nanomaterials in removing polycyclic aromatic hydrocarbon contaminants from water. Our experimental results indicate that GrO outperforms dendrimers in removing naphthalene from water. Molecular dynamics simulations suggest that the prominent factors driving naphthalene association to these seemingly disparate materials are similar. Interestingly, we find that cooperative interactions between the naphthalene molecules play a significant role in enhancing their association to the dendrimers and GrO. Our findings highlight that while selection of appropriate materials is important, the interactions between the contaminants themselves can also be important in governing the effectiveness of a given material. The combined use of experiments and molecular dynamics simulations allows us to comment on the possible factors resulting in better performance of GrO in removing polyaromatic contaminants from water.
    @Article{RSD:2015:EST,
    author = {Ryan S. DeFever and  Nicholas K. Geitner and Priyanka Bhattacharya,  and Feng Ding and Pu Chun Ke and Sapna Sarupria},
    title  = {{PAMAM dendrimers and graphene: Materials for removing aromatic contaminants from water}},
    journal  ={Environ. Sci. Technol.},
    year  ={2015},
    volume  = {Just Accepted},
    issue  = {},
    pages  = {},
    doi  = {10.1021/es505518r}
    }
    

2014

  1. Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water
    Amir Haji-Akbari, Ryan S. DeFever, Sapna Sarupria and Pablo G. Debenedetti, Phys. Chem. Chem. Phys., 16, 25916–25927, (2014)
    [Abstract] [BibTeX] [PDF]
    Freezing in the vicinity of water–vapor interfaces is of considerable interest to a wide range of disciplines, most notably the atmospheric sciences. In this work, we use molecular dynamics and two advanced sampling techniques, forward flux sampling and umbrella sampling, to study homogeneous nucleation of ice in free-standing thin films of supercooled water. We use a coarse-grained monoatomic model of water, known as mW, and we find that in this model a vapor–liquid interface suppresses crystallization in its vicinity. This suppression occurs in the vicinity of flat interfaces where no net Laplace pressure in induced. Our free energy calculations reveal that the pre-critical crystalline nuclei that emerge near the interface are thermodynamically less stable than those that emerge in the bulk. We investigate the origin of this instability by computing the average asphericity of nuclei that form in different regions of the film, and observe that average asphericity increases closer to the interface, which is consistent with an increase in the free energy due to increased surface-to-volume ratios.
    @Article{PGD:2014:PCCP,
    author = {Haji-Akbari, Amir and DeFever, Ryan S. and Sarupria, Sapna and Debenedetti, Pablo G.},
    title  = {Suppression of sub-surface freezing in free-standing thin films of a coarse-grained model of water},
    journal  ={Phys. Chem. Chem. Phys.},
    year  ={2014},
    volume  = {16},
    issue  = {47},
    pages  = {25916-25927},
    doi  = {10.1039/C4CP03948C}
    }
    

2013

  1. Molecular Dynamics Simulations of Peptide–SWCNT Interactions Related to Enzyme Conjugates for Biosensors and Biofuel Cells
    Karunwi O, and Baldwin C, and Griesheimer G, and Sarupria S and Guiseppi-Elie A, Nano LIFE, 3 (4), 1343007, (2013)
    [Abstract] [BibTeX] [PDF]
    With the demonstration of direct electron transfer between the redox active prosthetic group, flavin adenine dinucleotide (FAD), of glucose oxidase (GOx) and single-walled carbon nanotubes (SWCNT), there has been growing interest in the fabrication of CNT-enzyme supramolecular constructs that control the placement of SWCNTs within the tunneling distance of co-factors for enhanced electron transfer efficiency in generation-3 biosensors and advanced biofuel cells. These conjugate systems raise a series of questions such as: which peptide sequences within the enzymes have high affinity for the SWCNTs? And, are these high affinity sequences likely to be in the vicinity of the redox-active co-factor to allow for direct electron transfer? Phage display has recently been used to identify specific peptide sequences that have high affinity for SWCNTs. Molecular dynamics simulations were performed to study the interactions of five discrete peptides with (16,0) SWCNT in explicit water as well as with graphene. From the progression of the radius of gyration, Rg, the peptides studied were concertedly adsorbed to both the SWCNT and graphene. Peptide properties calculated using individual amino acid values, such as hydrophobicity indices, did not correlate with the observed adsorption behavior as quantified by Rg, indicating that the adsorption behavior of the peptide was not based on the individual amino acid residues. However, the Rg values, reflective of the physicochemical embrace of the surface (SWCNT or graphene) had a strong positive correlation with the solubility parameter, indicating concerted, cooperative interaction of peptide segments with the materials. The end residues appear to dominate the progression of adsorption regardless of character. Sequences identified by phage display share some homology with key enzymes (GOx, lactate oxidase and laccase) used in biosensors and enzyme-based biofuel cells. These analogous sequences appear to be buried deep within the shell of fully folded proteins and as such are expected to be close to the redox-active prosthetic group.
    @article{karunwi2013molecular,
      title   = {Molecular Dynamics Simulations of Peptide–SWCNT Interactions Related to Enzyme Conjugates for Biosensors and Biofuel Cells},
      author  = {Karunwi, Olukayode and Baldwin, Cassidy and Griesheimer, Gisela and Sarupria, Sapna and Guiseppi-Elie, Anthony},
      journal = {Nano LIFE},
      volume  = {03},
      number  = {04},
      pages   = {1343007},
      year    = {2013},
      doi     = {10.1142/S1793984413430071}		
    }
    
  2. SciFlow: A dataflow-driven model architecture for scientific computing using Hadoop
    Xuan P, and Zheng Y, and Sarupria S and Apon A, Big Data, 2013 IEEE International Conference on, 36-44, (2013)
    [Abstract] [BibTeX] [PDF]
    Many computational science applications utilize complex workflow patterns that generate an intricately connected set of output files for subsequent analysis. Some types of applications, such as rare event sampling, additionally require guaranteed completion of all subtasks for analysis, and place significant demands on the workflow management and execution environment. SciFlow is a user interface built over the Hadoop infrastructure that provides a framework to support the complex process and data interactions and guaranteed completion requirements of scientific workflows. It provides an efficient mechanism for building a parallel scientific application with dataflow patterns, and enables the design, deployment, and execution of data intensive, many-task computing tasks on a Hadoop platform. The design principles of this framework emphasize simplicity, scalability and fault-tolerance. A case study using the forward flux sampling rare event simulation application validates the functionality, reliability and effectiveness of the framework.
    @inproceedings{xuan2013sciflow,
      title   = {SciFlow: A dataflow-driven model architecture for scientific computing using Hadoop},
      author  = {Xuan, Pengfei and Zheng, Yueli and Sarupria, Sapna and Apon, Amy},
      booktitle={Big Data, 2013 IEEE International Conference on}, 
      pages   = {36-44},
      year    = {2013},
      doi     = {10.1109/BigData.2013.6691725}		
    }
    
  3. On the Thermodynamics and Kinetics of Hydrophobic Interactions at Interfaces
    Vembanur S, Patel AJ, Sarupria S and Garde S, J. Phys. Chem. B, 117 (35), 10261--10270, (2013)
    [Abstract] [BibTeX] [PDF]
    We have studied how primitive hydrophobic interactions between two or more small nonpolar solutes are affected by the presence of surfaces. We show that the desolvation barriers present in the potential of mean force between the solutes in bulk water are significantly reduced near an extended hydrophobic surface. Correspondingly, the kinetics of hydrophobic contact formation and breakage are faster near a hydrophobic surface than near a hydrophilic surface or in the bulk. We propose that the reduction in the desolvation barrier is a consequence of the fact that water near extended hydrophobic surfaces is akin to that at a liquid–vapor interface and is easily displaced. We support this proposal with three independent observations. First, when small hydrophobic solutes are brought near a hydrophobic surface, they induce local dewetting, thereby facilitating the reduction of desolvation barriers. Second, our results and those of Patel et al. ( Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 17678−17683) show that, whereas the association of small solutes in bulk water is driven by entropy, that near hydrophobic surfaces is driven by enthalpy, suggesting that the physics of interface deformation is important. Third, moving water away from its vapor–liquid coexistence, by applying hydrostatic pressure, leads to recovery of bulklike signatures (e.g., the presence of a desolvation barrier and an entropic driving force) in the association of solutes. These observations for simple solutes also translate to end-to-end contact formation in a model peptide with hydrophobic end groups, for which lowering of the desolvation barrier and acceleration of contact formation are observed near a hydrophobic surface. Our results suggest that extended hydrophobic surfaces, such as air–water or hydrocarbon–water surfaces, could serve as excellent platforms for catalyzing hydrophobically driven assembly.
    @article{vembanur2013thermodynamics,
      title   = {On the Thermodynamics and Kinetics of Hydrophobic 
                 Interactions at Interfaces},
      author  = {Vembanur, Srivathsan and Patel, Amish J and Sarupria, Sapna 
                 and Garde, Shekhar},
      journal = {J. Phys. Chem. B},
      volume  = {117},
      number  = {35},
      pages   = {10261--10270},
      year    = {2013},
      doi     = {10.1021/jp4050513}		
    }
    
  4. Exploiting the physicochemical properties of dendritic polymers for environmental and biological applications
    Bhattacharya P, and Geitner NK, and Sarupria S and Ke PC, Phys. Chem. Chem. Phys., 15 (13), 4477-4490, (2013)
    [Abstract] [BibTeX] [PDF]
    In this perspective we first examine the rich physicochemical properties of dendritic polymers for hosting cations, anions, and polyaromatic hydrocarbons. We then extrapolate these conceptual discussions to the use of dendritic polymers in humic acid antifouling, oil dispersion, copper sensing, and fullerenol remediation. In addition, we review the state-of-the-art of dendrimer research and elaborate on its implications for water purification, environmental remediation, nanomedicine, and energy harvesting.
    @article{bhattacharya2013physicochemical,
      title   = {Exploiting the physicochemical properties of dendritic polymers for environmental and biological applications},
      author  = {Bhattacharya, Priyanka and Geitner, Nicholas K. and Sarupria, Sapna and Ke, Pu Chun},
      journal = {Phys. Chem. Chem. Phys.},
      volume  = {15},
      number  = {13},
      pages   = {4477-4490},
      year    = {2013},
      doi     = {10.1039/C3CP44591G}		
    }
    

2012

  1. Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations
    Sarupria S and Debenedetti PG, The Journal of Physical Chemistry Letters, 3 (20), 2942-2947, (2012)
    [Abstract] [BibTeX] [PDF]
    We report atomistically detailed molecular dynamics simulations of homogeneous nucleation of methane hydrate in bulk aqueous phase in the absence of any interface. Subcritical clusters of water and methane molecules are formed in the initial segment of the simulations, which then aggregate to give the critical hydrate nucleus. This occurs over time scales of several hundred nanoseconds, indicating that the formation and aggregation of subcritical clusters can contribute significantly to the overall rate of hydrate nucleation. The clusters have elements of sI hydrate structure, such as 512 and 51262 cages as well as other uncommon 51263 and 51264 cages, but do not possess long-range order. Clusters are dynamic in nature and undergo continuous structural rearrangements.
    @article{sarupria2012homogeneous,
      title   = {Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations},
      author  = {Sarupria, Sapna and Debenedetti, Pablo G.},
      journal = {The Journal of Physical Chemistry Letters},
      volume  = {3},
      number  = {20},
      pages   = {2942-2947},
      year    = {2012},
      doi     = {10.1021/jz3012113}
    }
    

2011

  1. Molecular Dynamics Study of Carbon Dioxide Hydrate Dissociation
    Sarupria S and Debenedetti PG, The Journal of Physical Chemistry A, 115 (23), 6102-6111, (2011)
    [Abstract] [BibTeX] [PDF]
    We present results from a molecular dynamics study of the dissociation behavior of carbon dioxide (CO2) hydrates. We explore the effects of hydrate occupancy and temperature on the rate of hydrate dissociation. We quantify the rate of dissociation by tracking CO2 release into the liquid water phase as well as the velocity of the hydrate−liquid water interface. Our results show that the rate of dissociation is dependent on the fractional occupancy of each cage type and cannot be described simply in terms of overall hydrate occupancy. Specifically, we find that hydrates with similar overall occupancy differ in their dissociation behavior depending on whether the small or large cages are empty. In addition, individual cages behave differently depending on their surrounding environment. For the same overall occupancy, filled small and large cages dissociate faster in the presence of empty large cages than when empty small cages are present. Therefore, hydrate dissociation is a collective phenomenon that cannot be described by focusing solely on individual cage behavior.
    @article{sarupria2011molecular,
      title   = {Molecular Dynamics Study of Carbon Dioxide Hydrate Dissociation},
      author  = {Sarupria, Sapna and Debenedetti, Pablo G.},
      journal = {The Journal of Physical Chemistry A},
      volume  = {115},
      number  = {23},
      pages   = {6102-6111},
      year    = {2011},
      doi     = {10.1021/jp110868t}
    }
    

2010

  1. Studying pressure denaturation of a protein by molecular dynamics simulations
    Sarupria S, Ghosh T, Garcia AE and Garde S, Proteins, 78 (7), 1641-1651, (2010)
    [Abstract] [BibTeX] [PDF]
    Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This “unfolding-up-on-squeezing” is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results—that pressure denatured states are water-swollen, and theoretical results—that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states—their water-swollen nature, retention of secondary structure, and overall compactness—mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately −60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500–2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties and pressure stability of proteins, and can be potentially extended for applications to protein complexes and assemblies.
    @article{sarupria2010studying,
      title   = {Studying pressure denaturation of a protein by molecular 
                 dynamics simulations},
      author  = {Sarupria, Sapna and Ghosh, Tuhin and Garc{\'\i}a, Angel E 
                 and Garde, Shekhar},
      journal = {Proteins: Structure, Function, and Bioinformatics},
      volume  = {78},
      number  = {7},
      pages   = {1641--1651},
      year    = {2010},
      doi     = {10.1002/prot.22680}
    }
    

2009

  1. Hydrate Molecular Ballet
    Debenedetti PG and Sarupria S, Science, 326 (5956), 1070-1071, (2009)
    [Abstract] [BibTeX] [PDF]
    Hydrates are crystalline solids in which guest molecules are trapped within polyhedral water cages (1). They are important in hydrocarbon processing (2) and could play a major role in sustainable energy production (3, 4). Methane hydrate occurs naturally and in vast quantities on ocean floors and in permafrost, with implications for climate change and energy recovery (2). However, the molecular mechanisms leading to hydrate formation are poorly understood; this knowledge gap affects not just the science and technology of these materials, but our comprehension of hydrophobicity (5) and of disorder-order phase transitions. On page 1095 of this issue, Walsh et al. report a computational tour de force that offers a fascinating glimpse of the molecular events leading to methane hydrate formation (6).
    @article{debenedetti2009hydrate,
      title   = {Hydrate Molecular Ballet},
      author  = {Debenedetti, Pablo G. and Sarupria, Sapna},
      journal = {Science},
      volume  = {326},
      number  = {5956},
      pages   = {1070-1071},
      year    = {2009},
      doi     = {10.1126/science.1183027}
    }
    
  2. Addition/Correction: Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions
    Fennell CJ, Bizjak A, Vlachy V, Dill KA, Sarupria S, Rajamani S and Garde S, J. Phys. Chem. B, 113 (44), 14837-14838, (2009)
    [BibTeX] [PDF]
    @article{fennell2009addition,
      title   = {Ion pairing in molecular simulations of aqueous alkali halide solutions},
      author  = {Fennell, Christopher J. and Bizjak, Alan and Vlachy, Vojko and Dill, Ken A. and Sarupria, Sapna and Rajamani, Sowmianarayanan and Garde, Shekhar},
      journal = {J. Phys. Chem. B},
      volume  = {113},
      number  = {44},
      pages   = {14837-14838},
      year    = {2009},
      doi     = {10.1021/jp908484v}
    }
    
  3. Quantifying Water Density Fluctuations and Compressibility of Hydration Shells of Hydrophobic Solutes and Proteins
    Sarupria S and Garde S, Phys. Rev. Lett., 103(3), 37803, (2009)
    [Abstract] [BibTeX] [PDF]
    We probe the effects of solute length scale, attractions, and hydrostatic pressure on hydrophobic hydration shells using extensive molecular simulations. The hydration shell compressibility and water fluctuations both display a nonmonotonic dependence on solute size, with a minimum near molecular solutes and enhanced fluctuations for larger ones. These results and calculations on proteins suggest that the hydration shells of unfolded proteins are more compressible than of folded ones contributing to pressure denaturation. More importantly, the nonmonotonicity implies a solute curvature-dependent pressure sensitivity for interactions between hydrophobic solutes.
    @article{sarupria2009quantifying,
      title   = {Quantifying water density fluctuations and compressibility of hydration shells of hydrophobic solutes and proteins},
      author  = {Sarupria, Sapna and Garde, Shekhar},
      journal = {Physical review letters},
      volume  = {103},
      number  = {3},
      pages   = {037803},
      year    = {2009},
      doi     = {10.1103/PhysRevLett.103.037803}
    }
    

2008

  1. Enthalpy-Entropy Contributions to Salt and Osmolyte Effects on Molecular-Scale Hydrophobic Hydration and Interactions
    Athawale MV, Sarupria S and Garde S, J. Phys. Chem. B, 112(18), 5661-5670, (2008)
    [Abstract] [BibTeX] [PDF]
    Salts and additives can significantly affect the strength of water-mediated interactions in solution. We present results from molecular dynamics simulations focused on the thermodynamics of hydrophobic hydration, association, and the folding−unfolding of a hydrophobic polymer in water and in aqueous solutions of NaCl and of an osmolyte trimethylamine oxide (TMAO). It is known that addition of NaCl makes the hydration of hydrophobic solutes unfavorable and, correspondingly, strengthens their association at the pair as well as the many-body level (Ghosh, T.; Kalra, A.; Garde, S. J. Phys. Chem. B 2005, 109, 642), whereas the osmolyte TMAO has an almost negligible effect on the hydrophobic hydration and association (Athawale, M. V.; Dordick, J. S.; Garde, S. Biophys. J. 2005, 89, 858). Whether these effects are enthalpic or entropic in origin is not fully known. Here we perform temperature-dependent simulations to resolve the free energy into entropy and enthalpy contributions. We find that in TMAO solutions, there is an almost precise entropy−enthalpy compensation leading to the negligible effect of TMAO on hydrophobic phenomena. In contrast, in NaCl solutions, changes in enthalpy dominate, making the salt-induced strengthening of hydrophobic interactions enthalpic in origin. The resolution of total enthalpy into solute−solvent and solvent−solvent terms further shows that enthalpy changes originate primarily from solvent−solvent energy terms. Our results are consistent with experimental data on the hydration of small hydrophobic solutes by Ben-Naim and Yaacobi (Ben-Naim, A.; Yaacobi, M. J. Phys. Chem. 1974, 78, 170). In combination with recent work by Zangi, Hagen, and Berne (Zangi, R.; Hagen, M.; Berne, B. J. J. Am. Chem. Soc. 2007, 129, 4678) and the experimental data on surface tensions of salt solutions by Matubayasi et al. (Matubayasi, N.; Matsuo, H.; Yamamoto, K.; Yamaguchi, S.; Matuzawa, A. J. Colloid Interface Sci. 1999, 209, 398), our results highlight interesting length scale dependences of salt effects on hydrophobic phenomena. Although NaCl strengthens hydrophobic interactions at both small and large length scales, that effect is enthalpy-dominated at small length scales and entropy-dominated for large solutes and interfaces. Our results have implications for understanding of additive effects on water-mediated interactions, as well as on biocompatibility of osmolyte molecules in aqueous solutions.
    @article{athawale2008enthalpy,
      title   = {Enthalpy-entropy contributions to salt and osmolyte effects on 
                 molecular-scale hydrophobic hydration and interactions},
      author  = {Athawale, Manoj V and Sarupria, Sapna and Garde, Shekhar},
      journal = {The Journal of Physical Chemistry B},
      volume  = {112},
      number  = {18},
      pages   = {5661--5670},
      year    = {2008},
      doi     = {10.1021/jp073485n}
    }
    

2007

  1. Pressure dependence of the compressibility of a micelle and a protein: insights from cavity formation analysis
    Pereira B, Jain S, Sarupria S, Yang L and Garde S, Mol. Phys., 105 (2), 189-199, (2007)
    [Abstract] [BibTeX] [PDF]
    We present results from molecular dynamics simulations of a spherical micelle comprising 80 non-ionic C8E5 surfactants in water, a protein staphylococcal nuclease in water, and bulk n-hexane and water liquids over a range of hydrostatic pressures. We focus specifically on the pressure dependence of the volumetric properties—the partial molar volume and partial molar compressibility—of the micelle, the protein, and bulk liquids. We find that the micelle interior displays properties similar to liquid alkanes over a range of pressures and has a compressibility of 100−110×10−6 bar−1 under ambient conditions, which is more than twice that of liquid water. In contrast, the pressure dependence of the protein interior resembles that of solid organic polymeric materials and has a compressibility of 5−10×10−6 bar−1. We performed extensive analysis of cavity formation in all systems. Interestingly, it is not the average cavity size but the width of the cavity size distribution in a given medium that correlates with the compressibility of that medium over a broad range of pressures up to several kilobars. Correspondingly, the cavity size distribution is most sharply defined in protein interiors and is broadest in the micelle interior and in n-hexane. To explore the correlation between cavity formation and compressibility, we present preliminary calculations using the information theory approach in the bulk water phase. Analysis of cavity formation and, especially, the nature of the cavity size distribution may provide a sensitive probe of the compressibility and flexibility of local molecular environments in inhomogeneous condensed media.
    @article{pereira2007pressure,
      title   = {Pressure dependence of the compressibility of a micelle and a protein: insights from cavity formation analysis},
      author  = {Pereira, Brian and Jain, Sandeep and Sarupria, Sapna and Yang, Lu and Garde, Shekhar},
      journal = {Molecular Physics},
      volume  = {105},
      number  = {2-3},
      pages   = {189--199},
      year    = {2007},
      doi     = {10.1080/00268970601140750}
    }
    

For more details check out Prof. Sarupria's Google Scholar Profile