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Wang Y, Xie H, Alugubelli YR, Ma Y, Xu S, Ma J, Liu WR, Liang D. Accurate Mass Identification of an Interfering Water Adduct and Strategies in Development and Validation of an LC-MS/MS Method for Quantification of MPI8, a Potent SARS-CoV-2 Main Protease Inhibitor, in Rat Plasma in Pharmacokinetic Studies. Pharmaceuticals (Basel) 2022; 15:ph15060676. [PMID: 35745595 PMCID: PMC9228185 DOI: 10.3390/ph15060676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 12/04/2022] Open
Abstract
MPI8, a peptidyl aldehyde, is a potent antiviral agent against coronavirus. Due to unique tri-peptide bonds and the formyl functional group, the bioassay of MPI8 in plasma was challenged by a strong interference from water MPI8. Using QTOF LC-MS/MS, we identified MPI8•H2O as the major interference form that co-existed with MPI8 in aqueous and biological media. To avoid the resolution of MPI8 and MPI8•H2O observed on reverse phase columns, we found that a Kinetex hydrophilic interaction liquid chromatography (HILIC) column provided co-elution of both MPI8 and MPI8•H2O with a good single chromatographic peak and column retention of MPI8 which is suitable for quantification. Thus, a sensitive, specific, and reproducible LC-MS/MS method for the quantification of MPI8 in rat plasma was developed and validated using a triple QUAD LC-MS/MS. The chromatographic separation was achieved on a Kinetex HILIC column with a flow rate of 0.4 mL/min under gradient elution. The calibration curves were linear (r2 > 0.99) over MPI8 concentrations from 0.5−500 ng/mL. The accuracy and precision are within acceptable guidance levels. The mean matrix effect and recovery were 139% and 73%, respectively. No significant degradation of MPI8 occurred under the experimental conditions. The method was successfully applied to a pharmacokinetic study of MPI8 after administration of MPI8 sulfonate in rats.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA; (Y.W.); (H.X.); (J.M.)
| | - Huan Xie
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA; (Y.W.); (H.X.); (J.M.)
| | - Yugendar R. Alugubelli
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.R.A.); (Y.M.); (S.X.)
| | - Yuying Ma
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.R.A.); (Y.M.); (S.X.)
| | - Shiqing Xu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.R.A.); (Y.M.); (S.X.)
| | - Jing Ma
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA; (Y.W.); (H.X.); (J.M.)
| | - Wenshe R. Liu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA; (Y.R.A.); (Y.M.); (S.X.)
- Correspondence: (W.R.L.); (D.L.); Tel.: +1-979-845-1746 (W.R.L.); +1-713-313-1885 (D.L.)
| | - Dong Liang
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA; (Y.W.); (H.X.); (J.M.)
- Correspondence: (W.R.L.); (D.L.); Tel.: +1-979-845-1746 (W.R.L.); +1-713-313-1885 (D.L.)
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Ozaki Y, Beć KB, Morisawa Y, Yamamoto S, Tanabe I, Huck CW, Hofer TS. Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Chem Soc Rev 2021; 50:10917-10954. [PMID: 34382961 DOI: 10.1039/d0cs01602k] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.
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Affiliation(s)
- Yukihiro Ozaki
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan. and Toyota Physical and Chemical Research Institute, Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Krzysztof B Beć
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Yusuke Morisawa
- Department of Chemistry, School of Science and Engineering, Kindai University, Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Shigeki Yamamoto
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ichiro Tanabe
- Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80-82, A6020 Innsbruck, Austria
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Roy TK, Nagornova NS, Boyarkin OV, Gerber RB. A Decapeptide Hydrated by Two Waters: Conformers Determined by Theory and Validated by Cold Ion Spectroscopy. J Phys Chem A 2017; 121:9401-9408. [PMID: 29091429 DOI: 10.1021/acs.jpca.7b10357] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic level. We employ density functional calculations to compute a large pool of structures and vibrational spectra for a gas-phase complex, in which a doubly protonated decapeptide, gramicidin S, is solvated by two water molecules. Though most vibrations of this large complex are treated in a harmonic approximation, the water molecules and the vibrations of the host ion coupled to them are locally described by a quantum mechanical vibrational self-consistent field theory with second-order perturbation correction (VSCF-PT2). Guided and validated by the available cold ion spectroscopy data, the computational analysis identifies structures of the three experimentally observed conformers of the complex. They, mainly, differ by the hydration sites, of which the one at the Orn side chain is the most important for reshaping the peptide toward its native structure. The study demonstrates the ability of a quantum chemistry approach that intelligently combines the semiempirical and ab initio computations to disentangle a complex interplay of intra- and intermolecular hydrogen bonds in large molecular systems.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry & Chemical Sciences, Central University of Jammu , Jammu, 180011 India
| | - Natalia S Nagornova
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne , 1015 Lausanne, Switzerland
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University , Jerusalem 91904, Israel.,Department of Chemistry, University of California , Irvine, California 92697, United States.,Department of Chemistry, University of Helsinki , P.O. Box 55, 00014 Helsinki, Finland
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Baiardi A, Stein CJ, Barone V, Reiher M. Vibrational Density Matrix Renormalization Group. J Chem Theory Comput 2017; 13:3764-3777. [DOI: 10.1021/acs.jctc.7b00329] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alberto Baiardi
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Christopher J. Stein
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Vincenzo Barone
- Scuola Normale
Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Markus Reiher
- Laboratorium
für Physikalische Chemie, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Knaanie R, Šebek J, Tsuge M, Myllys N, Khriachtchev L, Räsänen M, Albee B, Potma EO, Gerber RB. Infrared Spectrum of Toluene: Comparison of Anharmonic Isolated-Molecule Calculations and Experiments in Liquid Phase and in a Ne Matrix. J Phys Chem A 2016; 120:3380-9. [DOI: 10.1021/acs.jpca.6b01604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roie Knaanie
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Jiří Šebek
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department
of Physical Chemistry, University of Chemistry and Technology, Prague 16628, Czech Republic
| | - Masashi Tsuge
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Nanna Myllys
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Leonid Khriachtchev
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Markku Räsänen
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
| | - Brian Albee
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - Eric O. Potma
- Department
of Chemistry, University of California, Irvine, California 92697, United States
| | - R. Benny Gerber
- Institute
of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department
of Chemistry, University of Helsinki, P.O. Box 55, FI-00014 Helsinki, Finland
- Department
of Chemistry, University of California, Irvine, California 92697, United States
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7
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Cheng X, Steele RP. Efficient anharmonic vibrational spectroscopy for large molecules using local-mode coordinates. J Chem Phys 2015; 141:104105. [PMID: 25217902 DOI: 10.1063/1.4894507] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
This article presents a general computational approach for efficient simulations of anharmonic vibrational spectra in chemical systems. An automated local-mode vibrational approach is presented, which borrows techniques from localized molecular orbitals in electronic structure theory. This approach generates spatially localized vibrational modes, in contrast to the delocalization exhibited by canonical normal modes. The method is rigorously tested across a series of chemical systems, ranging from small molecules to large water clusters and a protonated dipeptide. It is interfaced with exact, grid-based approaches, as well as vibrational self-consistent field methods. Most significantly, this new set of reference coordinates exhibits a well-behaved spatial decay of mode couplings, which allows for a systematic, a priori truncation of mode couplings and increased computational efficiency. Convergence can typically be reached by including modes within only about 4 Å. The local nature of this truncation suggests particular promise for the ab initio simulation of anharmonic vibrational motion in large systems, where connection to experimental spectra is currently most challenging.
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Affiliation(s)
- Xiaolu Cheng
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Largely reduced grid densities in a vibrational self-consistent field treatment do not significantly impact the resultingwavenumbers. Molecules 2014; 19:21253-75. [PMID: 25525825 PMCID: PMC6270979 DOI: 10.3390/molecules191221253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/25/2014] [Accepted: 12/09/2014] [Indexed: 11/16/2022] Open
Abstract
Especially for larger molecules relevant to life sciences, vibrational self-consistent field (VSCF) calculations can become unmanageably demanding even when only first and second order potential coupling terms are considered. This paper investigates to what extent the grid density of the VSCF’s underlying potential energy surface can be reduced without sacrificing accuracy of the resulting wavenumbers. Including single-mode and pair contributions, a reduction to eight points per mode did not introduce a significant deviation but improved the computational efficiency by a factor of four. A mean unsigned deviation of 1.3% from the experiment could be maintained for the fifteen molecules under investigation and the approach was found to be applicable to rigid, semi-rigid and soft vibrational problems likewise. Deprotonated phosphoserine, stabilized by two intramolecular hydrogen bonds, was investigated as an exemplary application.
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Lutz OMD, Rode BM, Bonn GK, Huck CW. The impact of highly correlated potential energy surfaces on the anharmonically corrected IR spectrum of acetonitrile. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:545-555. [PMID: 24840497 DOI: 10.1016/j.saa.2014.04.067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/20/2014] [Accepted: 04/13/2014] [Indexed: 06/03/2023]
Abstract
This paper discusses the quality and feasibility of highly correlated ab initio techniques in a vibrational self-consistent field (VSCF) approach using acetonitrile as a model system. The topical renormalized coupled-cluster technique exploiting the similarity-transformed Hamiltonian's left eigenstates (i.e. CR-CC(2,3)) is investigated alongside the well-known Hartree-Fock (HF), Møller-Plesset second-order perturbation theory (MP2) and coupled cluster (CCSD(T)) methods. The inclusion of mode triple interactions is discussed and it is found that the use of an effective core potential (ECP) serves as a viable compromise during the highly demanding task of computing such contributions, thus enabling a grid-based evaluation of three mode interaction terms with coupled cluster techniques also for larger molecules. In this context, a previously proposed reduced coupling scheme [1] is investigated, confirming the applicability of this technique to a system exhibiting a rather complex electronic structure. A combination of Ahlrichs' triple-ζ valence polarized (TZVP) basis set with Dunning's set of core-valence correlation functions is found to deliver results in good agreement with experiment while being computationally very feasible. Since CH3CN exhibits four degenerate vibrational degrees of freedom, it serves as an ideal model system for critically assessing the qualities of the degenerate second-order perturbation theory corrected (DPT2) VSCF technique. Besides fundamental vibrations, a thorough investigation of overtone transitions and combination bands is conducted by means of comparing the results to both available and newly recorded experimental data.
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Affiliation(s)
- Oliver M D Lutz
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Bernd M Rode
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Günther K Bonn
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian W Huck
- Institute of Analytical Chemistry and Radiochemistry, Center for Chemistry and Biomedicine, Leopold-Franzens University, Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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Knaanie R, Šebek J, Kalinowski J, Benny Gerber R. Hybrid MP2/MP4 potential surfaces in VSCF calculations of IR spectra: applications for organic molecules. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 119:2-11. [PMID: 23838574 DOI: 10.1016/j.saa.2013.06.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 05/20/2013] [Accepted: 06/08/2013] [Indexed: 06/02/2023]
Abstract
This study introduces an improved hybrid MP2/MP4 ab initio potential for vibrational spectroscopy calculations which is very accurate, yet without high computational demands. The method uses harmonic vibrational calculations with the MP4(SDQ) potential to construct an improved MP2 potential by coordinate scaling. This improved MP2 potential is used for the anharmonic VSCF calculation. The method was tested spectroscopically for four molecules: butane, acetone, ethylene and glycine. Very good agreement with experiment was found. For most of the systems, the more accurate harmonic treatment considerably improved the MP2 anharmonic results.
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Affiliation(s)
- Roie Knaanie
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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11
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Šebek J, Knaanie R, Albee B, Potma EO, Gerber RB. Spectroscopy of the C–H Stretching Vibrational Band in Selected Organic Molecules. J Phys Chem A 2013; 117:7442-52. [DOI: 10.1021/jp4014674] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jiří Šebek
- Institute
of Chemistry and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Roie Knaanie
- Institute
of Chemistry and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Brian Albee
- Department of Chemistry, University of California, Irvine, California
92697, United States
| | - Eric O. Potma
- Department of Chemistry, University of California, Irvine, California
92697, United States
| | - R. Benny Gerber
- Institute
of Chemistry and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California
92697, United States
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12
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Roy TK, Gerber RB. Vibrational self-consistent field calculations for spectroscopy of biological molecules: new algorithmic developments and applications. Phys Chem Chem Phys 2013; 15:9468-92. [DOI: 10.1039/c3cp50739d] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Šebek J, Pele L, Potma EO, Gerber RB. Raman spectra of long chain hydrocarbons: anharmonic calculations, experiment and implications for imaging of biomembranes. Phys Chem Chem Phys 2011; 13:12724-33. [PMID: 21670823 DOI: 10.1039/c1cp20618d] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
First-principles anharmonic vibrational calculations are carried out for the Raman spectrum of the C-H stretching bands in dodecane, and for the C-D bands in the deuterated molecule. The calculations use the Vibrational Self-Consistent Field (VSCF) algorithm. The results are compared with liquid-state experiments, after smoothing the isolated-molecule sharp-line computed spectra. Very good agreement between the computed and experimental results is found for the two systems. The combined theoretical and experimental results provide insights into the spectrum, elucidating the roles of symmetric and asymmetric CH(3) and CH(2) hydrogenic stretches. This is expected to be very useful for the interpretation of spectra of long-chain hydrocarbons. The results show that anharmonic effects on the spectrum are large. On the other hand, vibrational degeneracy effects seem to be rather modest at the resolution of the experiments. The degeneracy effects may have more pronounced manifestations in higher-resolution experiments. The results show that first-principles anharmonic vibrational calculations for hydrocarbons are feasible, in good agreement with experiment, opening the way for applications to many similar systems. The results may be useful for the analysis of CARS imaging of lipids, for which dodecane is a representative molecule. It is suggested that first-principles vibrational calculations may be useful also for CARS imaging of other systems.
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Affiliation(s)
- Jiří Šebek
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Iwamoto R. Infrared and Near-Infrared Study of the Interaction of Amide C═O with Water in Ideally Inert Medium. J Phys Chem A 2010; 114:7398-407. [DOI: 10.1021/jp102479t] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Reikichi Iwamoto
- NIRS Institute of Water, Yuyamadai 2-7-10, Kawanishi, Hyogo Pref. Japan
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Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. Phys Chem Chem Phys 2010; 12:4678-85. [DOI: 10.1039/b923041f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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16
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Zhang H, Siegrist K, Douglas KO, Gregurick SK, Plusquellic DF. THz investigations of condensed phase biomolecular systems. Methods Cell Biol 2009; 90:417-34. [PMID: 19195560 DOI: 10.1016/s0091-679x(08)00818-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Terahertz (THz) spectroscopic investigations of crystalline dipeptide nanotubes are discussed in the frequency region from 0.6 (2 cm(-1)) to 3 THz (100 cm(-1)). The THz region provides access to collective modes of biomolecular systems and is therefore sensitive to the large scale motions important for understanding the impact of environmental stimuli in biomolecular systems. The focus of this chapter is on THz spectral changes observed in this region when crystals of alanyl isoleucine (AI) and isoleucyl alanine (IA) nanotubes are exposed to water. Of biological significance is the water permeability through hydrophobic pore regions as exemplified in the disparate behavior of these two dipeptide nanotubes. AI is known from X-ray studies and confirmed here to act reversibly to the exchange of water while IA does not accept water into its pore region. Both quantum chemical and classical calculations are performed to better understand the subtle balance that determines guest molecule absorption and conduction through these hydrophobic channels. Examination of the vibrational character of the THz modes with and without water suggests water mode coupling/decoupling with collective modes of the nanotube may play an important role in the permeability dynamics.
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Affiliation(s)
- Hailiang Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA
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Gregurick SK, Kafafi SA. Computation of the Electronic and Spectroscopic Properties of Carbohydrates Using Novel Density Functional and Vibrational Self-Consistent Field Methods. J Carbohydr Chem 2008. [DOI: 10.1080/07328309908544041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Susan K. Gregurick
- a Center for Advanced Research in Biotechnology , University of Maryland Biotechnology Institute , 9600 Gudlesky Dr. Rockville MD 20742
| | - Sherif A. Kafafi
- a Center for Advanced Research in Biotechnology , University of Maryland Biotechnology Institute , 9600 Gudlesky Dr. Rockville MD 20742
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Doslić N, Kovacević G, Ljubić I. Signature of the Conformational Preferences of Small Peptides: a Theoretical Investigation. J Phys Chem A 2007; 111:8650-8. [PMID: 17691755 DOI: 10.1021/jp072565o] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An extensive computational study of the conformational preferences of N-acetylphenylalaninylamide (NAPA) is reported, including conformational and anharmonic frequency analyses, as well as calculations of excitation energies of the four NAPA conformers lowest in energy. Particular attention is paid to the influence of hydrogen-bonding interactions on the relative stability of the conformers, which was found to be very sensitive to both the level of quantum chemical computations and the anharmonic treatment of molecular vibrations. The assignments of the UV spectral peaks are well supported by the multireference CASSCF/MS-CASPT2 calculations. Upon consideration of the second-order Möller-Plesset (MP2) and density functional theory (DFT) structures, overall energetics, and harmonic and anharmonic corrections, we found no conclusive theoretical evidence for the assumed conformational propensity of small model peptides toward extended beta-strand structures.
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Affiliation(s)
- Nada Doslić
- Department of Physical Chemistry, Ruder Bosković Institute, Bijenicka cesta 54, Post Office Box 180, HR-10002, Zagreb, Republic of Croatia.
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Kwac K, Lee H, Cho M. Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra. J Chem Phys 2006; 120:1477-90. [PMID: 15268273 DOI: 10.1063/1.1633549] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.
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Affiliation(s)
- Kijeong Kwac
- Department of Chemistry and Center for Multidimensional Spectroscopy, Division of Chemistry and Molecular Engineering, Korea University, Seoul 136-701, Korea
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Gerber RB, Chaban GM, Gregurick SK, Brauer B. Vibrational spectroscopy and the development of new force fields for biological molecules. Biopolymers 2003; 68:370-82. [PMID: 12601796 DOI: 10.1002/bip.10293] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self-consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi-empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy.
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Affiliation(s)
- R B Gerber
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
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Gregurick SK, Chaban GM, Gerber RB. Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling ofN-Methylacetamide. J Phys Chem A 2002. [DOI: 10.1021/jp025633+] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Matsunaga N, Chaban GM, Gerber RB. Degenerate perturbation theory corrections for the vibrational self-consistent field approximation: Method and applications. J Chem Phys 2002. [DOI: 10.1063/1.1494978] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Chaban GM, Gerber RB. Ab initio calculations of anharmonic vibrational spectroscopy for hydrogen fluoride (HF)n (n = 3, 4) and mixed hydrogen fluoride/water (HF)n(H2O)n (n = 1, 2, 4) clusters. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2002; 58:887-898. [PMID: 11991501 DOI: 10.1016/s1386-1425(01)00676-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Anharmonic vibrational frequencies and intensities are computed for hydrogen fluoride clusters (HF)n, with n = 3, 4 and mixed clusters of hydrogen fluoride with water (HF)n(H2O)n where n = 1, 2. For the (HF)4(H2O)4 complex, the vibrational spectra are calculated at the harmonic level, and anharmonic effects are estimated. Potential energy surfaces for these systems are obtained at the MP2/TZP level of electronic structure theory. Vibrational states are calculated from the potential surface points using the correlation-corrected vibrational self-consistent field method. The method accounts for the anharmonicities and couplings between all vibrational modes and provides fairly accurate anharmonic vibrational spectra that can be directly compared with experimental results without a need for empirical scaling. For (HF)n, good agreement is found with experimental data. This agreement shows that the Møller-Plesset (MP2) potential surfaces for these systems are reasonably reliable. The accuracy is best for the stiff intramolecular modes, which indicates the validity of MP2 in describing coupling between intramolecular and intermolecular degrees of freedom. For (HF)n(H2O)n experimental results are unavailable. The computed intramolecular frequencies show a strong dependence on cluster size. Intensity features are predicted for future experiments.
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Affiliation(s)
- Galina M Chaban
- NASA Ames Research Center, Moffett Field, CA 94035-1000, USA.
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Bihary Z, Gerber RB, Apkarian VA. Vibrational self-consistent field approach to anharmonic spectroscopy of molecules in solids: Application to iodine in argon matrix. J Chem Phys 2001. [DOI: 10.1063/1.1384870] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Chaban GM, Jung JO, Gerber RB. Anharmonic Vibrational Spectroscopy of Hydrogen-Bonded Systems Directly Computed from ab Initio Potential Surfaces: (H2O)n, n = 2, 3; Cl-(H2O)n, n = 1, 2; H+(H2O)n, n = 1, 2; H2O−CH3OH. J Phys Chem A 2000. [DOI: 10.1021/jp993391g] [Citation(s) in RCA: 164] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Galina M. Chaban
- Department of Chemistry, University of California, Irvine, California 92697, and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Joon O. Jung
- Department of Chemistry, University of California, Irvine, California 92697, and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697, and Department of Physical Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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Chaban GM, Jung JO, Gerber RB. Ab initio calculation of anharmonic vibrational states of polyatomic systems: Electronic structure combined with vibrational self-consistent field. J Chem Phys 1999. [DOI: 10.1063/1.479452] [Citation(s) in RCA: 400] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Gregurick SK, Liu JHY, Brant DA, Gerber RB. Anharmonic Vibrational Self-Consistent Field Calculations as an Approach to Improving Force Fields for Monosaccharides. J Phys Chem B 1999. [DOI: 10.1021/jp9826221] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Broude S, Jung JO, Gerber R. Combined diffusion quantum Monte Carlo–vibrational self-consistent field (DQMC–VSCF) method for excited vibrational states of large polyatomic systems. Chem Phys Lett 1999. [DOI: 10.1016/s0009-2614(98)01296-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Chapo CJ, Paul JB, Provencal RA, Roth K, Saykally RJ. Is Arginine Zwitterionic or Neutral in the Gas Phase? Results from IR Cavity Ringdown Spectroscopy. J Am Chem Soc 1998. [DOI: 10.1021/ja982991a] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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