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Vibrational spectroscopic map

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Vibrational spectroscopic maps are a series of ab initio, semiempirical, or empirical models tailored to specific IR probes to describe vibrational solvatochromic effects on molecular spectra quantitatively.[1]

Coherent multidimensional spectroscopy,[2][3] a nonlinear spectroscopy utilizing multiple time-delayed pulses, is a technique that enables the measurement of solvation-induced frequency shifts and the time-correlations of the fluctuating frequencies. Researchers employ various organic and biochemical methods to introduce small vibrational probes into molecular systems into a variety of chemicals, proteins, nucleic acids, etc.[4] These probes, labeled with infrared (IR) markers, were subject to spectroscopic investigations to obtain quantitative insights into various features of chemical and biological systems. In general, interpreting the experimental multidimensional spectra to get information on the underlying molecular processes requires theoretical modeling.[5]

The vibrational frequency shifts observed due to complex intermolecular interactions of small IR probes with surroundings in the condensed phase are minute, often representing fractions of thermal energy. Numerical accuracy associated with advanced quantum mechanical calculations are not sufficient to accurately model these shifts.[6] Consequently, researchers commonly resort to mapping procedures, which correlate certain physical variables calculated for the probe molecule with spectroscopic properties such as vibrational frequencies. These mapping procedures are referred to as vibrational spectroscopic maps within the field.

Typically, the physical variables employed in vibrational frequency maps include electric potentials, electric fields, distributed higher multipole moments, and other relevant factors evaluated at specific points surrounding the molecule.

As an example, the vibrational frequency associated with a localized vibrational mode is correlated with the electrostatic potential and electric field values at a designated set of points known as distributed sites within the infrared (IR) chromophore.[7]

Theoretical foundation

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The vibrational frequency shift, denoted as , for the jth normal mode of a given probe molecule is defined as the difference between the actual vibrational frequency   of the mode in a solution and the frequency  in the gas phase.

ref name=":2">Buckingham, A. D. (1960). "Solvent effects in vibrational spectroscopy". Transactions of the Faraday Society. 56: 753. doi:10.1039/tf9605600753. ISSN 0014-7672.</ref>.[8][9][10][11]

From an effective Hamiltonian for the solute in the presence of molecular environment, one can derive the effective vibrational force constant (or Hessian) matrix approximately as follows:[11][12]

where the subscript 0 means the quantity is evaluated at the gas-phase geometry.

In the limiting case that the vibrational couplings of the normal mode of interest with other vibrational modes are relatively weak, the vibrational frequency shift under such a weak coupling approximation (WCA) in solution from the gas-phase frequency is given by[13][11]

Here, and are the electric anharmonicity (EA) and mechanical anharmonicity (MA) operators, respectively. These operators are defined as

and

By substituting a relevant expression for the intermolecular interaction potential into the WCA expression for , one can derive the vibrational frequency shift based on the specific theoretical potential model under consideration.

Semiempirical approaches

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While several rigorous theories for vibrational solvatochromism based on physical approximations have been proposed,[1] these sophisticated models often necessitate extensive quantum chemistry calculations performed at elevated levels of precision with a large basis set. Current electronic structure simulation methods fall short in providing vibrational frequencies directly comparable to experimentally measured frequency shifts, especially when they are on the order of a few wavenumbers.[14][15]

To accurately calculate coefficients in vibrational solvatochromism expressions, researchers frequently turn to employing multivariate leastsquare fitting. This technique involves fitting a sufficiently extensive set of training data obtained from quantum chemistry calculations of vibrational frequency shifts for numerous clusters containing a solute and multiple solvent molecules.

An early approach aimed to express the solvation-induced vibrational frequency shift in terms of the solvent electric potentials evaluated at distributed atomic sites on the target solute molecule.[4] This method involves calculating the solvent electric potentials at these specific solute sites through the utilization of atomic partial charges from surrounding solvent molecules. The vibrational frequency shift of the solute molecule, denoted as , for the jth vibrational mode can be represented as[10][7]

Here, represents the vibrational frequency of the jth normal mode in solution, signifies the vibrational frequency in the gas phase, N denotes the number of distributed sites on the solute molecule, denotes the solvent electric potential at the kth site of the solute molecule, and are the parameters to be determined through least-square fitting to a training database comprising clusters containing a solute and multiple solvent molecules. This method provides a means to quantify the impact of solvation on the vibrational frequencies of the solute molecule.

Another widely used model for characterizing vibrational solvatochromic frequency shifts involves expressing the frequency shift in terms of solvent electric fields evaluated at distributed sites on the target solute molecule.[4][16][17]

Developments

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Vibrational spectroscopic maps have been developed for a diverse range of vibrational modes, including various molecular systems and functional groups.[1][4] Some of the notable vibrational modes include:

  • Amide I mode of NMA (N-Methylacetamide)[7][17]
  • Amide I mode of peptide molecules[18][19][20][21]
  • Amide I vibration of isotope-labeled proteins[22][23][24]
  • Amide II vibration[25]
  • Nitrile (CN) stretch[26][27]
  • Thiocyanato (SCN) stretch[26][27]
  • Selenothiocyanato (SeCN) stretch[28]
  • Azido (N3) stretch[29]
  • Carbonmonoxy (CO) stretch[30]
  • Ester carbonyl (O-C=O) stretch[31]
  • Carbonate carbonyl (C=O) stretch[32]
  • Water OH and OD stretch[33][34][35]
  • C-D stretch[36]
  • S=O stretch[37]
  • Phosphate (PO2) stretch[38][39]
  • Nucleic acid base modes[40]
  • OH and OD stretch mode in alcohols[41]
  • Water bending mode[42]

References

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  1. ^ a b c Baiz, Carlos R.; Błasiak, Bartosz; Bredenbeck, Jens; Cho, Minhaeng; Choi, Jun-Ho; Corcelli, Steven A.; Dijkstra, Arend G.; Feng, Chi-Jui; Garrett-Roe, Sean; Ge, Nien-Hui; Hanson-Heine, Magnus W. D.; Hirst, Jonathan D.; Jansen, Thomas L. C.; Kwac, Kijeong; Kubarych, Kevin J. (2020-08-12). "Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction". Chemical Reviews. 120 (15): 7152–7218. doi:10.1021/acs.chemrev.9b00813. ISSN 0009-2665. PMC 7710120. PMID 32598850.
  2. ^ Cho, Minhaeng (2009). Two-dimensional optical spectroscopy. Boca Raton, Fla.: CRC Press. ISBN 978-1-4200-8429-0.
  3. ^ Hamm, Peter; Zanni, Martin T. (2011). Concepts and methods of 2d infrared spectroscopy. Cambridge: Cambridge university press. ISBN 978-1-107-00005-6.
  4. ^ a b c d Kim, Heejae; Cho, Minhaeng (2013-08-14). "Infrared Probes for Studying the Structure and Dynamics of Biomolecules". Chemical Reviews. 113 (8): 5817–5847. doi:10.1021/cr3005185. ISSN 0009-2665. PMID 23679868.
  5. ^ Mukamel, Shaul (2009). Principles of nonlinear optical spectroscopy. Oxford series in optical and imaging sciences. New York: Oxford Univ. Press. ISBN 978-0-19-513291-5.
  6. ^ Sax, Alexander F. (April 2008). "Computational Chemistry techniques: covering orders of magnitude in space, time, and accuracy". Monatshefte für Chemie - Chemical Monthly. 139 (4): 299–308. doi:10.1007/s00706-007-0827-7. ISSN 0026-9247. S2CID 85451980.
  7. ^ a b c Ham, Sihyun; Kim, Joo-Hee; Lee, Hochan; Cho, Minhaeng (2003-02-22). "Correlation between electronic and molecular structure distortions and vibrational properties. II. Amide I modes of NMA–nD2O complexes". The Journal of Chemical Physics. 118 (8): 3491–3498. doi:10.1063/1.1536980. ISSN 0021-9606.
  8. ^ Buckingham, A. D. (1958-11-11). "Solvent effects in infra-red spectroscopy". Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences. 248 (1253): 169–182. Bibcode:1958RSPSA.248..169B. doi:10.1098/rspa.1958.0237. ISSN 0080-4630. S2CID 97510562.
  9. ^ Buckingham, A. D. (1960-03-22). "A theory of frequency, intensity and band-width changes due to solvents in infra-red spectroscopy". Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences. 255 (1280): 32–39. Bibcode:1960RSPSA.255...32B. doi:10.1098/rspa.1960.0046. ISSN 0080-4630. S2CID 95330195.
  10. ^ a b Cho, Minhaeng (2003-02-22). "Correlation between electronic and molecular structure distortions and vibrational properties. I. Adiabatic approximations". The Journal of Chemical Physics. 118 (8): 3480–3490. Bibcode:2003JChPh.118.3480C. doi:10.1063/1.1536979. ISSN 0021-9606.
  11. ^ a b c Cho, Minhaeng (2009-03-07). "Vibrational solvatochromism and electrochromism: Coarse-grained models and their relationships". The Journal of Chemical Physics. 130 (9). Bibcode:2009JChPh.130i4505C. doi:10.1063/1.3079609. ISSN 0021-9606. PMID 19275407.
  12. ^ Jeon, Jonggu; Yang, Seongeun; Choi, Jun-Ho; Cho, Minhaeng (2009-09-15). "Computational Vibrational Spectroscopy of Peptides and Proteins in One and Two Dimensions". Accounts of Chemical Research. 42 (9): 1280–1289. doi:10.1021/ar900014e. ISSN 0001-4842. PMID 19456096.
  13. ^ Buckingham, A. D. (1960). "Solvent effects in vibrational spectroscopy". Transactions of the Faraday Society. 56: 753. doi:10.1039/tf9605600753. ISSN 0014-7672.
  14. ^ Helgaker, Trygve; Jørgensen, Poul; Olsen, Jeppe (2012). Molecular electronic-structure theory (Repr. as paperback ed.). Chichester Weinheim: Wiley. ISBN 978-1-118-53147-1.
  15. ^ McArdle, Sam; Mayorov, Alexander; Shan, Xiao; Benjamin, Simon; Yuan, Xiao (2019). "Digital quantum simulation of molecular vibrations". Chemical Science. 10 (22): 5725–5735. doi:10.1039/C9SC01313J. ISSN 2041-6520. PMC 6568047. PMID 31293758.
  16. ^ Corcelli, S. A.; Lawrence, C. P.; Skinner, J. L. (2004-05-01). "Combined electronic structure/molecular dynamics approach for ultrafast infrared spectroscopy of dilute HOD in liquid H2O and D2O". The Journal of Chemical Physics. 120 (17): 8107–8117. doi:10.1063/1.1683072. ISSN 0021-9606. PMID 15267730.
  17. ^ a b Schmidt, J. R.; Corcelli, S. A.; Skinner, J. L. (2004-11-08). "Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches". The Journal of Chemical Physics. 121 (18): 8887–8896. Bibcode:2004JChPh.121.8887S. doi:10.1063/1.1791632. ISSN 0021-9606. PMID 15527353.
  18. ^ Bouř, Petr; Keiderling, Timothy A. (2003-12-01). "Empirical modeling of the peptide amide I band IR intensity in water solution". The Journal of Chemical Physics. 119 (21): 11253–11262. Bibcode:2003JChPh.11911253B. doi:10.1063/1.1622384. ISSN 0021-9606.
  19. ^ Hahn, Seungsoo; Lee, Hochan; Cho, Minhaeng (2004-07-22). "Theoretical calculations of infrared absorption, vibrational circular dichroism, and two-dimensional vibrational spectra of acetylproline in liquids water and chloroform". The Journal of Chemical Physics. 121 (4): 1849–1865. Bibcode:2004JChPh.121.1849H. doi:10.1063/1.1763889. ISSN 0021-9606. PMID 15260736.
  20. ^ Choi, Jun-Ho; Hahn, Seungsoo; Cho, Minhaeng (January 2005). "Amide I IR, VCD, and 2d IR spectra of isotope-labeled α-helix in liquid water: Numerical simulation studies". International Journal of Quantum Chemistry. 104 (5): 616–634. Bibcode:2005IJQC..104..616C. doi:10.1002/qua.20543. ISSN 0020-7608.
  21. ^ Watson, Tim M.; Hirst *, Jonathan D. (2005-06-10). "Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin". Molecular Physics. 103 (11–12): 1531–1546. Bibcode:2005MolPh.103.1531W. doi:10.1080/00268970500052387. ISSN 0026-8976. S2CID 93817942.
  22. ^ Reppert, Mike; Tokmakoff, Andrei (2016-05-27). "Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics". Annual Review of Physical Chemistry. 67 (1): 359–386. Bibcode:2016ARPC...67..359R. doi:10.1146/annurev-physchem-040215-112055. ISSN 0066-426X. PMID 27023758.
  23. ^ Buchanan, Lauren E.; Dunkelberger, Emily B.; Tran, Huong Q.; Cheng, Pin-Nan; Chiu, Chi-Cheng; Cao, Ping; Raleigh, Daniel P.; de Pablo, Juan J.; Nowick, James S.; Zanni, Martin T. (2013-11-26). "Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient β-sheet". Proceedings of the National Academy of Sciences. 110 (48): 19285–19290. Bibcode:2013PNAS..11019285B. doi:10.1073/pnas.1314481110. ISSN 0027-8424. PMC 3845187. PMID 24218609.
  24. ^ Woys, Ann Marie; Almeida, Aaron M.; Wang, Lu; Chiu, Chi-Cheng; McGovern, Michael; de Pablo, Juan J.; Skinner, James L.; Gellman, Samuel H.; Zanni, Martin T. (2012-11-21). "Parallel β-Sheet Vibrational Couplings Revealed by 2D IR Spectroscopy of an Isotopically Labeled Macrocycle: Quantitative Benchmark for the Interpretation of Amyloid and Protein Infrared Spectra". Journal of the American Chemical Society. 134 (46): 19118–19128. doi:10.1021/ja3074962. ISSN 0002-7863. PMC 3523199. PMID 23113791.
  25. ^ Maekawa, Hiroaki; Ge, Nien-Hui (2010-01-28). "Comparative Study of Electrostatic Models for the Amide-I and -II Modes: Linear and Two-Dimensional Infrared Spectra". The Journal of Physical Chemistry B. 114 (3): 1434–1446. doi:10.1021/jp908695g. ISSN 1520-6106. PMID 20050636.
  26. ^ a b Choi, Jun-Ho; Oh, Kwang-Im; Lee, Hochan; Lee, Chewook; Cho, Minhaeng (2008-04-02). "Nitrile and thiocyanate IR probes: Quantum chemistry calculation studies and multivariate least-square fitting analysis". The Journal of Chemical Physics. 128 (13). Bibcode:2008JChPh.128m4506C. doi:10.1063/1.2844787. ISSN 0021-9606. PMID 18397076.
  27. ^ a b Oh, Kwang-Im; Choi, Jun-Ho; Lee, Joo-Hyun; Han, Jae-Beom; Lee, Hochan; Cho, Minhaeng (2008-04-21). "Nitrile and thiocyanate IR probes: Molecular dynamics simulation studies". The Journal of Chemical Physics. 128 (15). Bibcode:2008JChPh.128o4504O. doi:10.1063/1.2904558. ISSN 0021-9606. PMID 18433232.
  28. ^ Yamada, Steven A.; Thompson, Ward H.; Fayer, Michael D. (2017). "Water-anion hydrogen bonding dynamics: Ultrafast IR experiments and simulations". The Journal of Chemical Physics. 146 (23). Bibcode:2017JChPh.146w4501Y. doi:10.1063/1.4984766. hdl:1808/27375. PMID 28641416. Retrieved 2024-02-20.
  29. ^ Choi, Jun-Ho; Oh, Kwang-Im; Cho, Minhaeng (2008-11-07). "Azido-derivatized compounds as IR probes of local electrostatic environment: Theoretical studies". The Journal of Chemical Physics. 129 (17). Bibcode:2008JChPh.129q4512C. doi:10.1063/1.3001915. ISSN 0021-9606. PMID 19045363.
  30. ^ Choi, Jun-Ho; Kwak, Kyung-Won; Cho, Minhaeng (2013-12-12). "Computational Infrared and Two-Dimensional Infrared Photon Echo Spectroscopy of Both Wild-Type and Double Mutant Myoglobin-CO Proteins". The Journal of Physical Chemistry B. 117 (49): 15462–15478. doi:10.1021/jp405210s. ISSN 1520-6106. PMID 23869523.
  31. ^ Edington, Sean C.; Flanagan, Jennifer C.; Baiz, Carlos R. (2016-06-09). "An Empirical IR Frequency Map for Ester C═O Stretching Vibrations". The Journal of Physical Chemistry A. 120 (22): 3888–3896. Bibcode:2016JPCA..120.3888E. doi:10.1021/acs.jpca.6b02887. ISSN 1089-5639. PMID 27214642.
  32. ^ Liang, Chungwen; Kwak, Kyungwon; Cho, Minhaeng (2017-12-07). "Revealing the Solvation Structure and Dynamics of Carbonate Electrolytes in Lithium-Ion Batteries by Two-Dimensional Infrared Spectrum Modeling". The Journal of Physical Chemistry Letters. 8 (23): 5779–5784. doi:10.1021/acs.jpclett.7b02623. ISSN 1948-7185. PMID 29131650.
  33. ^ Corcelli, S. A.; Lawrence, C. P.; Skinner, J. L. (2004-05-01). "Combined electronic structure/molecular dynamics approach for ultrafast infrared spectroscopy of dilute HOD in liquid H2O and D2O". The Journal of Chemical Physics. 120 (17): 8107–8117. doi:10.1063/1.1683072. ISSN 0021-9606. PMID 15267730.
  34. ^ Hayashi, Tomoyuki; la Cour Jansen, Thomas; Zhuang, Wei; Mukamel, Shaul (2005-01-01). "Collective Solvent Coordinates for the Infrared Spectrum of HOD in D 2 O Based on an ab Initio Electrostatic Map". The Journal of Physical Chemistry A. 109 (1): 64–82. Bibcode:2005JPCA..109...64H. doi:10.1021/jp046685x. ISSN 1089-5639. PMID 16839090.
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  36. ^ Kinnaman, Carrie S.; Cremeens, Matthew E.; Romesberg, Floyd E.; Corcelli, Steven A. (2006-10-01). "Infrared Line Shape of an α-Carbon Deuterium-Labeled Amino Acid". Journal of the American Chemical Society. 128 (41): 13334–13335. doi:10.1021/ja064468z. ISSN 0002-7863. PMID 17031927.
  37. ^ Oh, Kwang-Im; Baiz, Carlos R. (2019-12-17). "Empirical S=O stretch vibrational frequency map". The Journal of Chemical Physics. 151 (23). Bibcode:2019JChPh.151w4107O. doi:10.1063/1.5129464. ISSN 0021-9606. PMID 31864235.
  38. ^ Floisand, D. J.; Corcelli, S. A. (2015-10-15). "Computational Study of Phosphate Vibrations as Reporters of DNA Hydration". The Journal of Physical Chemistry Letters. 6 (20): 4012–4017. doi:10.1021/acs.jpclett.5b01973. ISSN 1948-7185. PMID 26722770.
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  40. ^ Jiang, Yaoyukun; Wang, Lu (2019-07-11). "Development of Vibrational Frequency Maps for Nucleobases". The Journal of Physical Chemistry B. 123 (27): 5791–5804. doi:10.1021/acs.jpcb.9b04633. ISSN 1520-6106. PMC 6820520. PMID 31260308.
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  42. ^ Ni, Yicun; Skinner, J. L. (2015-07-07). "IR and SFG vibrational spectroscopy of the water bend in the bulk liquid and at the liquid-vapor interface, respectively". The Journal of Chemical Physics. 143 (1): 014502. Bibcode:2015JChPh.143a4502N. doi:10.1063/1.4923462. ISSN 0021-9606. PMID 26156483.
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