Spectroscopie vibrationnelle et simulations de dynamique moléculaire - Effet de l environnement sur les propriétés spectroscopiques - PDF

Description
Spectroscopie vibrationnelle et simulations de dynamique moléculaire - Effet de l environnement sur les propriétés spectroscopiques DFT-MD & QM-MM-DFT-MD ATIGE Prof. Marie-Pierre Gaigeot

Please download to get full document.

View again

of 42
All materials on our website are shared by users. If you have any questions about copyright issues, please report us to resolve them. We are always happy to assist you.
Information
Category:

Music & Video

Publish on:

Views: 4 | Pages: 42

Extension: PDF | Download: 0

Share
Transcript
Spectroscopie vibrationnelle et simulations de dynamique moléculaire - Effet de l environnement sur les propriétés spectroscopiques DFT-MD & QM-MM-DFT-MD ATIGE Prof. Marie-Pierre Gaigeot Brief introduction on molecular dynamics simulations for vibrational spectroscopy Principes de la Spectroscopie vibrationnelle Lumière incidente Mlilieu absorbant Lumière transmise Spectre d aborption InfraRouge (IR) ou de diffusion Raman mesuré comme réponse du milieu à la stimulation par la lumière incidente (champ électrique, laser) Une molécule = un ensemble d oscillateurs Les vibrations : réponse des ressorts aux sollicitations avec des mouvements identifiés (4 types généraux) Oscillateur libre Oscillateur contraint par une liaison hydrogène DFT-based molecular dynamics simulations for the modeling of vibrational spectra Interest/motivation : structure and dynamics of complex molecular finite T vibrational spectroscopy : powerful probe of structures & dynamics (fingerprints) - One-to-one relationship between vibrational fingerprints and structure/dynamics - We want to understand/interpret the experimental spectra in terms of structure and dynamics (and more ) : can not be achieved by experiments alone - Achieve predictive accuracy : ab initio MD is required We systematically couple experiments and simulations Standard IR spectra calculations in literature : 0K Quantum Chemistry Molecules of biological interest ( 10 atoms, amino acids, peptides ) 1 st assumption : classical nuclei Geometry optimisation : search for minima on the PES - molecules are frozen in their optimized geometry (0 K) - PES : 3N-6 degrees of freedom - tricky for complex molecules & floppy molecules Normal modes calculation for each equilibrium geometry - diagonalize a essian matrix - expensive calculation for big systems harmonic approximation Calculation of transition dipole derivatives for IR intensities The Fermi Golden Rule reduces to harmonic approximation Matching to experiment? Beyond harmonic approximations, still at 0K R.B. Gerber, A. McCoy, D.A. Benoit (CC-VSCF) experiment Standard IR spectra calculations in literature : 0K Quantum Chemistry Main drawbacks : - search for the minima of lowest energy on the potential energy surface PES : 3N-6 degrees of freedom tricky for complex molecules, for floppy molecules - 0 K approximation the molecules are frozen in their optimized geometry crude approximation for molecules which can undergo conformational dynamics at finite temperature - essian diagonalisation to be performed for each isomer - The double harmonic approximations what about anharmonic modes? - Difficult to take into account the condensed phase : solutes in liquid water mimick the liquid phase with a few -bonded water molecules : but this is no bulk! Standard IR spectra calculations in literature : 0K Quantum Chemistry Another drawback (not the least ) : Calculations have to be performed for each identified minimum on the PES Check which signatures are compatible with experimental signatures Then decide, which conformer(s) «explain(s)» the experimental features Expensive in CPU time, sometimes difficult to perform for complex floppy molecules experiment Standard IR spectra calculations in literature : 0K Quantum Chemistry Obviously, these remarks depend whether the associated experiments are performed at 0 K or at finite temperature (300 K) [ See next slides ] When do we expect anharmonicities? - high frequency regime 2500 cm -1 : N- or O- bonds involved in hydrogen bonding - low frequency domain, far IR cm -1 delocalized modes, strongly anharmonic, mainly torsions - Whenever there are mode couplings Theoretical methods that go beyond the harmonic approximation : VSCF method of Benny Gerber : still very expensive for big systems Molecular Dynamics : this is the methodology we have developed Beyond harmonic 0K calculations : DFT-MD for Vibrational Spectroscopy (review of our work, 25 papers since 2003) IRMPD EXP IR DFT-MD Gas phase in relation with Action Spectroscopy exps IR-MPD & IR-PD at finite temperature Peptides Ala n + (n=2 10) Solutes immersed in liquid water in relation with exps IR, Raman (DFT-MD & QM-MM-MD) Peptides Ala n, peptide peridinin Interfaces in relation with non-linear SFG exps Oxides Si/water, Al/water, water/air, Boehmite/water/Peptide Direct modelling of vibrational spectroscopy signals & interpretation in terms of atomic movements and couplings Beyond traditional Quantum Chemistry calculations & beyond harmonic approximations Temperature taken into account : pivotal for flexible/floppy molecules like peptides Environments mandatory to be taken into account for vibrational features : liquids & interfaces Anharmonicities taken into account in DFT-MD PCCP Review/Perspective 2010 Excellent agreements of theoretical dynamical spectra with experiments & precise interpretations/assignments of bands in terms of conformational dynamics, dynamics of bonds, anharmonicities, couplings to environments Beyond Quantum Chemistry & introducing temperature & dynamics Statistical Mechanics and Linear Response Theory: The Fermi Golden Rule can be expressed as No approximation M(t) : total dipole at time t Linear Response Theory framework The whole spectrum is obtained in one single calculation { Band positions Band intensities Band shapes This is the domain of finite temperature molecular dynamics simulations Everything is contained in the fluctuations of the dipole moment Comparisons to experiments done on the whole spectrum Beyond Quantum Chemistry & introducing temperature & dynamics Statistical Mechanics and Linear Response Theory: The Fermi Golden Rule can be expressed as No approximation M(t) : total dipole at time t Linear Response Theory framework The whole spectrum is obtained in one single calculation { Band positions Band intensities Band shapes This is the domain of finite temperature molecular dynamics simulations Everything is contained in the fluctuations of the dipole moment Comparisons to experiments done on the whole spectrum All anharmonicities included - dynamics on all accessible parts of the PES (harm + given T - no harmonic approximation for dipole - mode-couplings taken into account IR spectrum takes into account the ensemble of conformations explored along the dynamics: average over the conformations - minima + all other structures - relative weigths from dynamics sampling Only limitation : quality of the ab initio representation DFT/BLYP works pretty well Other reasons for MD being mandatory for theoretical vibrational spectroscopy Gas phase : Action finite temperature IR-MPD, IR-PD set-ups FEL cm -1 : CLIO/France (Maitre, Ohanessian), FELIX/Netherlands (Oomens, von elden) OPO cm -1 : Simons/Snoek Oxford, Lisy, Duncan, Jonhson USA Low T : Rizzo Lausanne, Mons Paris Room temperature, internal energy vibrational spectroscopy : powerful probe of structures & dynamics (fingerprints) Structures & Dynamics are pivotal for the interpretation of IR-(M)PD spectra, Especially for floppy peptides Molecular dynamics mandatory Condensed phase (liquids, finite temperature Bulk must be included for reliable fingerprints J.Phys.Chem.B. 107:10344 (2003) J.Phys.Cond. Matt. In Press (2011) Bulk : minimum of energy has no signification - Thermal fluctuations are mandatory Room temperature, internal energy, solvent couplings & fluctuations Molecular dynamics mandatory ab-initio Molecular Dynamics Z k Classical nuclei Electronic clouds BO approximation Schrödinger equation Newton/Lagrange dynamics Z i Z l Two approaches in the DFT framework : Born-Oppenheimer MD (CP2K code) & Car-Parrinello MD (CPMD code) Use of Wannier Centers in order to calculate molecular dipoles (IR) & molecular polarisability tensors (Raman, SFG) 100' atoms - 10' pico-seconds Wannier centers for IR spectroscopy Molecular dipoles are calculated using the localised Wannier centers Localised Wannier Centers Wannier orbitals are obtained through a unitary transformation of KS orbitals minimising their spatial extent : Wannier centers = localised electrons on individual molecules of the system Partition of molecular dipoles & molecular IR spectra Wannier centers : dipoles O, N : Lone pairs Double bond : 2 Wannier centers Single bond : 1 Wannier center Average dipole of liquid water D Trans NMA : 6.96±0.58 D Cis NMA : 7.33±0.48 D Illustrations des calculs de dynamique moléculaire ab initio à température finie pour la spectroscopie vibrationnelle IR Illustrations issues de nos travaux de recherche Environmental effects on vibrational spectroscopy Gas phase spectroscopy of peptides : neighbours on the chain are environment and can influence the vibrational features Spectroscopy of peptides in the liquid phase : influences from the liquid water environment Spectroscopy of peptides in the liquid phase : influences from different liquid environments Spectroscopy at solid-liquid interfaces : how the surface modulates properties of solvent, and vice versa Gas phase spectroscopy In relation with IR-MPD experiments IRMPD 300K gas phase spectroscopy of the Ala 2 + peptide J.Phys.Chem.A. 110, (2006) - Collaboration J.P. Schermann, C. Desfrançois, G. Grégoire Villetaneuse a model system: the protonated dialanine peptide E kcal/mol trans O1 proton transfer kcal/mol + trans A2 C-Terminal rotation most stable conformers 0 K transa1 + IRMPD 300K gas phase spectroscopy of the Ala 2 + peptide J.Phys.Chem.A. 110, (2006) - Collaboration J.P. Schermann, C. Desfrançois, G. Grégoire Villetaneuse a model system: the protonated dialanine peptide E kcal/mol trans O1 proton transfer kcal/mol + trans A2 C-Terminal rotation most stable conformers 0 K transa1 + Exp. IR-MPD spectrum: contributions from different isomers? IRMPD 300K gas phase spectroscopy of the Ala 2 + peptide CPMD at 300 K Continuous isomerisation dynamics between 2 conformers transa1 et transa2 ϕ ϕ ϕ transa1 = -162 transa2 = - 74 A2 A1 The relative weight of each conformation probed during the dynamics will be naturally taken into account in the calculation of the infrared spectrum Gas phase IR-MPD of Ala 2 + peptide: conformational dynamics Exp: J.P. Schermann, C. Desfrançois, G. Grégoire Villetaneuse : Continuous conformational dynamics between 2 conformers transa1 et transa2 ϕ ϕ ϕ transa1 = -162 transa2 = - 74 A2 + + A1 A1 A2 Free energy profile measured along the dynamics No energy barrier in going from transa1 to transa2 ΔG 0.3 kcal/mol The relative weight of all conformations probed during the dynamics will be naturally taken into account in the calculation of the infrared spectrum Gas phase IR-MPD of Ala 2 + peptide: conformational dynamics proton transfer between trans A1-A2 and trans O1 in the gas phase 2 3 Proton transfer events naturally taken into account in the IR spectrum calculation d O 1 d O 2 d O 3 IRMPD 300K gas phase spectroscopy of the Ala 2 + peptide Exp. MD δ(c=o), δ(co), ν(n-c) δ(n 3+ ), ν(c=o) backbone δ(n-) the calculated spectrum reflects experimental features band intensities : -? (no direct comparison) Calc. signal : stationary IR Exp. signal : fragmentation yield ν(c=o), ν(c-n) Finite temperature MD is useful for the IR spectroscopy calculation of floppy molecules ν(c=o) Average over 10 different dynamics J.Phys.Chem.A. 110, (2006) Gas phase IR-MPD Ala3+ : dynamics of -bonds Coll. Oxford Snoek, Vaden, de Boer - Paper JCTC 2009 N2 unfolded family : 2N -N 50% dyns CO.. O=C proton hops in between N3+ unfolded family : N3+ O=C : 50% proton transfers == N2 extremity Thermal rotation of N3+ & COO extremity Static harmonic calculations C- O- N- (no N-+) N3+ folded family : Thermal rotation of N3+, breaking/forming of bond MD simulations, JCTC 5:1068(2009) Exp. Spectrum features result from all conformations - Coexistence in the exp. + Conformational dyn. The dynamics of the N- groups bonds give rise to the complex cm-1 band Diversity of anharmonicities of N N2 & N..OC -bonds probed == complex broad band due to immediate neighbours = environment N-+ stretch highly anharmonic, red-shifted from cm-1 domain Gas phase IR-MPD Ala 7 + : N- + anharmonicities directly probed Exps. Oxford Snoek, Vaden, de Boer ; DFT-MD : IJMS 2011 (in press) 1(N + O) 2(N + O) 3(N + O) Ala The supplementary cm : Loss of vibrational anharmonicities of the N-+ stretch comes when going from 1 N + O bond from to 3 N + O bonds the loss of anharmonicities of N- + stretching DFT-MD of Ala K : globular structures on average with 2 N- + O bonds & 1 N- + O bond as the most probable conformations 3 N + O bonds can exist but are less likely and far less stable Spectral features here : record the environmental effects [ how many bonds formed by N 3 + terminal ] Liquid phase spectroscopy in relation with IR experiments IR spectroscopy of solutes in liquid water: bulk effects IR spectrum [Wannier Centers] Amide I Amide II δ(c-), δ(n-c) δ(n-), ν(n-c) Amide III + skeleton stretches NMA + 50 water molecules 9.00 ps dynamics - DFT-MD ν(n-c 3 ), δ(n-), δ(c-) N 2-Ala immersed in 118W 100 ps dynamics DFT-MD Amide I-II bands Discrepencies observed : bands related to methyls DFT : dispersion 2-Ala in Water : direct evidence for PII/beta conformations Direct proof of Trans-NMA in solution Such agreements validate the arrangements of water molecules around solutes (first hydration shell & beyond) J.Chem.Theor.Comput. 1, (2005) All trajectories : PII/beta + alphar alphar trajectories PII/beta trajectories J.Phys.Chem.B Letters 113:10059 (2009) ; P.C.C.P. 12:10198 (2010) Peridinin solvent molecules ps dynamics - QM(solute)-MM(solvent) MD Solvents : acetonitrile, methanol, cyclohexane (different polarities/aproticities) Band-Shifts depending on solvent: reproduce exps. Explicit solvent mandatory In Press PCCP 2011, Coll. Guidoni Rome Vibrational Spectroscopy of Peridinin peptide immersed in different liquids IR spectroscopy of peridinin peptide in different liquids Coll. Leonardo Guidoni, Daniele Bovi, Riccardo Spezia, Alberto Mezetti, PCCP in press (2011) Peridinin : carbonyl-containing carotenoids, of particular interest in photophysics Debate on lactonic C=O band and relation with its local environment Peridinin : different local environments in the full protein (PCP Peridinin Chlorophyll Complex) Cover picture, PCCP Mimicked here by different surrounding solvents Cyclohexane deuterated Acetonitrile Methanol Apolar/aprotic Polar/aprotic Polar/protic QM-MM-MD simulations : PBE (BOMD)/Amber CPMD code, 1000 solvent molecules, 20 ps Peridinin : QM ; All solvent : MM Carbonyl shift Solvent effects QM/MM-MD simulations Vibrational shifts in excellent agreement with red-shifts observed in Raman exps in the same solvents Vibrational red-shifts follow the organisation and strengths of solvent around the C=0 Static DFT with implicit solvent No -bond Solvent CX 3 Polarity Weak -bond ACN 35 MET 31 Strong -bond Need explicit -bonds and -bond dynamics Assignment in biological environment By inspecting the X-ray structure we can look for groups around lactonic C=O. From g(r) of MD, we can identify relevant distances and characterize each Per as CX-, ACN- or MET-like Per 611 : no -bonds, apolar environment Per 612 : no -bonds, polar environment Per 623 : -bond, polar/protic environment Spectroscopy at solid/liquid interfaces In relation with VSFG experiments (non-linear) Vibrational solid/water interface Coll. M. Sulpizi (Mainz, Germany), M. Sprik (Cambridge, UK), In Press in J. Phys. Cond Matt α-quartz Surface (0001) α-quartz : (0001) hexagonal Surface Supercell : X X Å 3 Fully hydroxilated surface α-alumina Surface (0001) α-alumina (corundum) : R-3c space group Supercell : X X Å 3 Fully hydroxilated surface the quartz/water interface VSFG : Vibrational Sum Frequency Generation, non-linear spectroscopy necessicates both IR & Raman activities of modes VSFG : sensitive to interface species only (inactive in pure liquids) VSFG exps : O- intramolecular stretching motions probed VSFG : water layers probed Exps : Shen et al. (USA) Debated assignments in literature : - Liquid-like vs Ice-like - Water directly adjacent to surface vs Water in the following layers - 4-coordinated water vs under-coordinated water DFT-based MD finite temperature is a good way to investigate structure, dynamics and spectroscopy cm cm -1 Exps. Shen et al. (USA) ( 0001 ) α-quartz Surface α-quartz : (0001) hexagonal Surface Supercell : X X Å 3 Fully hydroxilated surface PBC : 11 Å gap between the surfaces W accep O O W donor O O Dried surface : In-plane zig-zags of -bonds between hydroxyl groups (. same for alumina ) Effect of solvent environment Wet surface : In-plane Si-O and Out-of-plane Si-O now exist and alternate - Both are interacting with liquid water at the interface (1st layer of solvent above the surface) Organisation of water at solid interfaces : 2 case : silica oxide/ and alumina oxide/ water interfaces W accep O O W donor W accep O O W donor O O O O Interface Quartz/eau liquide Interface Aluminium/eau liquide Water donor Liquid Water Water acceptor w O(Sil) B 1.82 Å Ow w B 1.81 Å Ow O(Al) B 2.00 Å w-ow 0.988Å «liquid like» w-ow 0.990Å «liquid like» w-ow Å «Weak bonds» Water acceptor «icelike» Ice «icelike» Ow (Sil) B 1.64 Å Ow w B 1.76 Å w-ow 0.996Å «Strong bonds» w-ow 0.999Å Water donor w O(Al) B 1.70 Å w-ow Å Reversal of role & properties of water molecules acceptor/donor of bonds at the 2 interfaces Vibrational IR signatures at solid/liquid interfaces : water Coll. M. Sulpizi (Mainz, Germany), M. Sprik (Cambridge, UK), In Press in J. Phys. Cond Matt Interface Quartz/liquid water Intermediate bonds Strong bonds Weak bonds Interface Alumina/liquid water Strong bonds Intermediate bonds Weak bonds O O O O O O O O OW-acceptor : Strong bonds «ice-like» O O O O W-donor : Weak bonds «liquid-like» W-donor : Strong bonds «ice-like» O O O O OW-acceptor : Weak bonds «liquid-like» Reversal of -bond signatures between the two interfaces : donor/acceptor - weak/strong -bonds Interpretation of SFG signatures from DFT-MD of the interfaces (true signal under calculation) Quartz-water & Alumina-water interface : some conclusions Strongly adsorbed water the surface pkas in very good agreement with exps. Linear IR spectroscopy Useful information obtained wrt VSFG Literature debates on 3400/3200 cm -1 peaks : - Water directly adjacent to surface/following layers - 4-coordinated water/under-coordinated water - Liquid-like/Ice-like interface : strength of bonds, nature of bonds responsible for signals has been put forward Relationship between pkas and IR peak positions work in progress Collaborators on these works : Amel Sediki (Part-time Post-Doc, 2010) Alvaro Cimas-Samaniego (Post-Doc 2009, now in Portugal) Codruta Marinica (Post-Doc 2006, now MdC at LCAM-Orsay France) Michaël Martinez (PhD 2007, now Post-Doc in eidelberg Germany) Michiel Sprik - Cambridge UK Marialore Sulpizi - Mainz Germany Nick Besley - University of Nottingham UK - Alliance Program Rodolphe Vuilleumier, Daniel Borgis ENS France Dominique Costa - ENSCP France, Alessandro Motta, Italy Van Oahn Nguyen-Thi, LCP Orsay, Pascal Parneix, ISMO Orsay Group of JP Schermann, G Grégoire, C Desfrançois - Villetaneuse France Groups of P Maître & G Ohanessian - Orsay France - ANR PROBIO Group of JP Simons, L. Snoek, T. Vaden - Oxford UK - Alliance Program Group of J Lisy - Urbana-Champaign USA - ANR International/NSF program 2011 A selection of References on these works D. Bovi, A. Mezzetti, R. Vuilleumier, M.-P. Gaigeot, B. Chazallon, R. Spezia, L. Guidoni, Environmental Effects on Vibrational Properties of Carotenoids : Experiments and Calculations on Peridinin In Press in Phys. Chem. Chem. Phys., DOI : /C1CP21985E A. Sediki, L. C. Snoek, M.-P. Gaigeot Intermolecular vibrational anharmonicities directly revealed from DFT-based molecular dynamics simulations of the Ala7+ protonated peptide. In Press in Int. J. Mass Spectrom., http ://dx.doi.org/ /j.ijm
Related Search
We Need Your Support
Thank you for visiting our website and your interest in our free products and services. We are nonprofit website to share and download documents. To the running of this website, we need your help to support us.

Thanks to everyone for your continued support.

No, Thanks