Probing the structure of a rotaxane with two-dimensional infrared spectroscopy.

Femtosecond 2D-IR spectroscopy has been used to study the structure of a [2]rotaxane composed of a benzylic amide macrocycle that is mechanically interlocked onto a succinamide-based thread. Both the macrocycle and the thread contain carbonyl groups, and by determining the coupling between the stretching modes of these groups from the cross-peaks in the 2D-IR spectrum, the structure of the macrocycle-thread system has been probed. Our results demonstrate that 2D-IR spectroscopy can be used to observe structural changes in molecular devices on a picosecond time scale.

[1]  O. Golonzka,et al.  Coupling and orientation between anharmonic vibrations characterized with two-dimensional infrared vibrational echo spectroscopy , 2001 .

[2]  Stoddart,et al.  Artificial Molecular Machines. , 2000, Angewandte Chemie.

[3]  Albert Stolow,et al.  Multidimensional Snapshots of Chemical Dynamics , 2004, Science.

[4]  G. Bodenhausen,et al.  Principles of nuclear magnetic resonance in one and two dimensions , 1987 .

[5]  L. Nafie Infrared and Raman vibrational optical activity: theoretical and experimental aspects. , 1997, Annual review of physical chemistry.

[6]  Andrei Tokmakoff,et al.  Two-dimensional infrared spectroscopy of antiparallel beta-sheet secondary structure. , 2004, Journal of the American Chemical Society.

[7]  A. Tokmakoff Two-Dimensional Line Shapes Derived from Coherent Third-Order Nonlinear Spectroscopy , 2000 .

[8]  R. Hochstrasser,et al.  Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[9]  P. Hamm,et al.  A two-dimensional infrared study of localization, structure, and dynamics of a dipeptide in membrane environment. , 2004, Biophysical journal.

[10]  R. Hochstrasser,et al.  Two-dimensional IR spectroscopy can be designed to eliminate the diagonal peaks and expose only the crosspeaks needed for structure determination , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[11]  J. Fraser Stoddart,et al.  A Molecular Elevator , 2004, Science.

[12]  Francesco Zerbetto,et al.  Unidirectional rotation in a mechanically interlocked molecular rotor , 2003, Nature.

[13]  R. Hochstrasser,et al.  Dynamics of amide-I modes of the alanine dipeptide in D2O. , 2005, The journal of physical chemistry. B.

[14]  S. Woutersen,et al.  Vibrational relaxation of the bending mode of HDO in liquid D2O. , 2005, The journal of physical chemistry. A.

[15]  S. Ham,et al.  Local Amide I Mode Frequencies and Coupling Constants in Polypeptides , 2003 .

[16]  R. Hochstrasser,et al.  The two-dimensional IR nonlinear spectroscopy of a cyclic penta-peptide in relation to its three-dimensional structure. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[17]  David Bebbington,et al.  A Molecular Brake , 1994 .

[18]  R. Hochstrasser,et al.  STRUCTURE OF THE AMIDE I BAND OF PEPTIDES MEASURED BY FEMTOSECOND NONLINEAR-INFRARED SPECTROSCOPY , 1998 .

[19]  T. Keiderling,et al.  Solvent effects on IR and VCD spectra of helical peptides: DFT-based static spectral simulations with explicit water. , 2005, Journal of Physical Chemistry B.

[20]  James R Heath,et al.  Whence Molecular Electronics? , 2004, Science.

[21]  Richard A. Silva,et al.  Unidirectional rotary motion in a molecular system , 1999, Nature.

[22]  Euan R Kay,et al.  Electrochemically switchable hydrogen-bonded molecular shuttles. , 2003, Journal of the American Chemical Society.

[23]  William H. Press,et al.  Numerical recipes in C , 2002 .

[24]  Jeffrey S. Moore,et al.  Design and Synthesis of a “Molecular Turnstile” , 1995 .

[25]  Euan R. Kay,et al.  A Reversible Synthetic Rotary Molecular Motor , 2004, Science.

[26]  Jean-Pierre Sauvage,et al.  Molecular Catenanes, Rotaxanes and Knots , 1999 .

[27]  Amber T. Krummel,et al.  Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy. , 2004, The Journal of chemical physics.

[28]  David J. Williams,et al.  Anion‐Assisted Self‐Assembly , 1997 .

[29]  Gerhard Stock,et al.  Hydrogen-bond lifetime measured by time-resolved 2D-IR spectroscopy: N-methylacetamide in methanol , 2001 .

[30]  N. Harada,et al.  Light-driven monodirectional molecular rotor , 2022 .

[31]  Peter Hamm,et al.  Structure Determination of Trialanine in Water Using Polarization Sensitive Two-Dimensional Vibrational Spectroscopy , 2000 .

[32]  S. Mukamel Principles of Nonlinear Optical Spectroscopy , 1995 .

[33]  D. Jonas Optical Analogs of 2D NMR , 2003, Science.

[34]  N. Demirdöven,et al.  Correlated vibrational dynamics revealed by two-dimensional infrared spectroscopy. , 2002, Physical review letters.

[35]  Francesco Zerbetto,et al.  Photoisomerization of a rotaxane hydrogen bonding template: Light-induced acceleration of a large amplitude rotational motion , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[36]  C. Renner,et al.  Transient 2D-IR spectroscopy: Snapshots of the nonequilibrium ensemble during the picosecond conformational transition of a small peptide , 2003 .

[37]  Joshua Jortner,et al.  Vibrational relaxation of a molecule in a dense medium , 1973 .

[38]  J. Bandekar,et al.  Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins. , 1986, Advances in protein chemistry.

[39]  Andrei Tokmakoff,et al.  Conformational changes during the nanosecond-to-millisecond unfolding of ubiquitin. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Thomas Schrader,et al.  Functional Synthetic Receptors , 2005 .

[41]  F. Paolucci,et al.  Photoinduction of Fast, Reversible Translational Motion in a Hydrogen-Bonded Molecular Shuttle , 2001, Science.

[42]  R. Kubo Statistical Physics II: Nonequilibrium Statistical Mechanics , 2003 .

[43]  M. Cho,et al.  Molecular dynamics simulation study of N-methylacetamide in water. II. Two-dimensional infrared pump–probe spectra , 2003 .

[44]  Robin M. Hochstrasser,et al.  Two-dimensional heterodyned and stimulated infrared photon echoes of N-methylacetamide-D , 2001 .

[45]  P. Atkins,et al.  Molecular Quantum Mechanics , 1970 .

[46]  Amber T. Krummel,et al.  Inter and Intrastrand Vibrational Coupling in DNA Studied with Heterodyned 2D-IR Spectroscopy , 2003 .