Nano-confinement of biomolecules: hydrophilic

confinement promotes structural order and enhances

mobility of water molecules

Bachir Aoun1 and Daniela Russo2,3 ( )

Nano Res., Just Accepted Manuscript DOI: 10.1007/s12274-015-0907-7 http://www.thenanoresearch.com on Oct. 9, 2015 Tsinghua University Press 2015

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NanoResearch DOI10.1007/s1227401509077

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ctronicpplementarydparameterdsion op://dx.doi.org

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Quirke, N.; carbon pipes.

,

;

,

,

NCM

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2 CN

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Electro

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achir Aoun1 a

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.Various fordinordertor reproductionMA solutionby using

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model interargesweredeoundsandwinorder toa

hilic nces

MM22,havealforcefieldofNAGMAtions wereed variant

actionwithrivedfrom

water. achieve the

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objectivesofourstructuralanddynamicalinvestigation. Theinitialconfigurations.Simulationswerecarriedoutat295KusingdifferentconcentrationsofNagmaandNalmasolutions intheNPTensemble.TheLangevinpistonmethod isusedtocontrolthepressure,withanintegrationtimestepof1fs.Threedimensionalcubicperiodicboundaryconditionswereappliedwitha longdistances interactioncutoff fixedat12using theParticleMeshEwald (PME)methodwasusedforthelongrangecoulombforcescalculation.Thetotalnumberofsolutemolecules(Nagma,Nalma)wasfixedat100andthenumbersofwatermoleculeswereadjustedaccordingtothedesiredconcentration[Table II]. The initial configurationswere constructed to be as dispersed as possible in order to avoidaggregation. Finally, energyminimization and 5ns of equilibrationwere performed and followed by aproduction runof1ns thatwasused forcomparison toexperimentaldata.While theTIP3watermodelseems togivea ratherhighdiffusionconstant compared to theexperiment, theNalma solutediffusionmatchestheexperimentaldiffusioncoefficient[TableSII].

Table SII: Molecular dynamics parameter of Nagma and Nalma molecules in water solution

CHARMM22parameters&

experimentalvalues

Nalma1:252M

Nalma1:501M

Nagma1:193M

Nagma1:501M

Solutemoleculesnumber 100 100 100 100

Watermoleculesnumber 2554 5000 1948 5000

Meanboxlength(A) 47.4 56.3 42.4 55.1

Simulationwater D(105cm2s1)

2.7 3.5 3.25 3.9

Simulationsolute D(105cm2s1)

0.33 0.4 0.78 0.91

Experimentwater** D(105cm2s1)

0.75 1.26 1.1 1.65

Experimentsolute** D(105cm2s1)

0.31 0.36

**Difusionconstantsderivedfromreference[3,4]However, as themain focus of thiswork is on the solute behavior,we only qualitatively compare thedynamicalparametersofthewatermolecules.

FigureS1a)andS1b)reporttheatomisticrepresentationsoftwoinitialconditionsthathavebeentestedinordertoperformsimulationonthewholeSWCNTandbiomoleculesystem.FigureS1a)isbuildfromanequilibratedsolutionstateofNalmaorNagmawhichhavebeenpreviouslyused tochoice theusedpotential.Adding an empty SWCNT in thebox,wenoticed that the final equilibration timewasextremely long (over200ns),becausewatermolecules first fill theSWCNTand then theyare replacedfrom the biomolecules. For this reason a different strategywas used. Figure S1b) shows the randomgeneratedsystemwherewatermoleculesandbiomoleculespartiallyfilltheSWCNTas initialcondition.

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Duringtheequilibration,thebiomolecules immediately loadtheSWCNTandthetotalstabilizationtimewasoftheorderof100ns.Therefore,weusedthissetupforourcalculation.

It is important tonote thatdifferent lengthsanddiametersofSWCNThavebeenalso tested inorder to control themolecules structuredependence from the size of thenanotube.Weverified that acutoffof1.5nmenables the fillingof theSWCNTwith thebiomoleculesandbeyond2.0nmabove, thestructuralbehavioranddonotseemstochange.IndependencefromtheCNTlengthhasbeenalsoverifiedup to 10 nm. Consequently, in order to improve the simulation time/performancewe decided to useSWCNTof4nmdiameterand5nmlong

a) b)

Figure S1. a) Initial condition builds from the final equilibrated state of bio-molecules in solution, at the desired concentration,

and an empty SWCNT. The equilibration state is reached after 200 ns. b) Initial condition builds from a randomly generated

systems containing SWCNT, water molecules and bio-molecule at the desired concentration. The equilibration state is reached in a

time range of 100 ns. Both configuration s represent the Nagma molecule case.

Structure. Inorder to comparewith theXraydiffraction structure factor andwithpreviousmoleculardynamicssimulations[2]wealsocalculatedtheI(Q)Xrayscatteringfunction[FigureS2].Thepeaksandshiftspositionsasa functionofsolventconcentrationagreewith theexperimentalresults [2].Therefore,increasingtheconcentration,weobservedthatthemainpeakatQ~1.8A1ofNalmasolution,decreaseinintensity and shifts to lowerQvalueswhile thebump atQ~0.8A1 ismorepronounced.An equivalent

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behaviorisalsoobservedfortheNagmasolution,forwhatthemaindiffractionpeakisconcerned.

Figure S2: Simulated X-ray scattering intensity pattern for Nagma and Nalma as a function of concentration, in water solutions.

Axial and transverseMSDs. Inordertoconfirm theconsistencyofourresultsandconclusionswealsocalculated theaxialand transversediffusion forbothNalma/waterandNagma/watersystems.Confinedatoms and molecules in SWCNT axial and transversal MSD components, are computed upon the

transformedcoordinates totheSWCNTprincipalaxesreferentialsystem .As ,

and arethemain,secondaryandtertiaryprincipalaxes,atomsinsidetheSWCNTarestripedoutofthe

globalSWCNTdiffusionbyapplyingthefollowingtimedependenttransformationmatrixMT

And

ThereforeintheSWCNTprincipalaxesreferentialsystem,axialMSDarecomputedupon and

transversalMSDupon vectorsandthetotalMSDsisnowthesumbetweentheaxialandthe

transverseMSDs.From thewater confinement point of view (Figure S3a)we found that transversal diffusion ofwatermolecules isdominantup to1nswhileaxialdiffusion takesoveroverconfirming thepresenceand theexternalexchangeofthewatermoleculesinthechannel.Inaddition,resultsreportedinFigureS3bshow,forNagmamolecules,animportanttransversediffusionascomparedtotheaxialdiffusion,inthewholeobservedtimeframe.

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For Nalma and the few trapped water molecules, diffusion is remarkably different compare toNagma/water confinement. First the few water molecules which have been confined (Figure S3c),essentiallyexperiencealocaltranslationaldiffusion(likelylocal,consideringthemagnitudeoftheMSD)andshowaquitenegligibleaxialdiffusion.Atthesametime,Nalmamoleculesarecharacteristicofahighlysuppressedaxialdiffusionandapronouncedlocaltransversediffusion(FigureS3d). Alsointhisnewcalculation,asalreadynoticeableinFigure6a),Nalma/waterMSDsaresignificantlowerandwithadifferenttimedependencecomparedtoNagma/watersystem.

a b

c dFigure S3) Axial, transverse and total MSDs calculated for a) water confined with Nagma molecules; b) Nagma molecules; c)

water confined with Nalma molecules; d) Nalma molecules

Parameterdefinitions

NumberDensityND(t):Itistheratiobetweenthenumberofatomsoftargetmoleculesfoundina

definedspacebythevolumeofthisspaceataspecifictime .Thiscalculationisusefultostudy

theevolutionintermofquantityofaminoacidscomparedtowaterinsidethenanotubes.ND(t)iscalculatedfollowingeq.(1):

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isthevolumeofthenanotube, representstheatomsselection, definesthenumberof

atomsfoundinsidethenanotubeattime .

Mean Shell Thickness,MST(t): It is the average of all the target atoms radii in the nanotube

cylinderattime .Thisparameterhasbeenusedtostudyhowaminoacidscompetewithwater

insidethenanotube.MST(t)iscalculatedusingeq.(2):

While referstotheatomicspeciesand totheSWCNT, isthetotalnumberoftarget

atoms found inside the SWCNT at time . is the distance between the atom and the

SWCNTmainaxisattime

CylindricalDensityDistribution, CDD(d):Describes the ratio of cylindrical densities of atoms

inside the nanotube at a distance from the nanotubemain axis of symmetry. CDD(d) is

calculatedusingeq(3)

Where isthetotalnumberoftargetatomsfoundinsidethenanotubeattime , represents

theSWCNTvolume, thedistanceoftheselectedatom fromtheaxis. isthenanotubelength,

while istheradialdistancetoleranceand istheKroneckerdeltathat isequalto1

when andequaltozeroelsewhere.

MeanSquareDisplacement,MSD(t):Thisparametergivesinformationaboutthespatialextentof

randommotionofthemolecules.MSD(t)iscalculatedusingeq.(4)

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Where denotestheaverageoverallatomsand and thepositionsoftheatomattime

and .WhentheMSDshowsalineardependencefromthetimet,thediffusioncoefficient canbe

calculatedfromeq.(5):

TheMSD data Figure 6a)were calculated directly from the trajectories and from those dataweinferredthediffusioncoefficientcalculatedinthetimeintervalupto1ns

HydrogenBondAnalysis:Ahydrogenbondisanattractiveforcethatoccurswhenanhydrogenis

bound toanelectronegativeatoms.Therefore, it canbedefinedbetween exactly threeatoms,adonor,thehydrogenandanacceptor.Thedonorisanelectronegativeatom(e.g.oxygen,nitrogen,fluorine)withanegativecharge,covalentlybondedtothehydrogenatom.Theacceptorisalsoanelectronegativeatom thatbelongs to the samemoleculeas thedonorand thehydrogenor toacompletelydifferentmolecule. In thisworkwe investigatewaterhydrogenbondeddimers confined incarbonnanotube.Anoxygendonoratomofawatermoleculesharesanyofthetwohydrogenofthesamemoleculewithanacceptoroxygenatomofanearwatermolecule. Inourcomputation,weconsider the following criteria to decide whether an HB is formed: hydrogenacceptor BondLength(BL)