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Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024; 45:1846-1869. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
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Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
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2
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Reese DL, Steele RP. Molecular Motion in the Interconverting σ-H 2, Di-, and Tri-hydride Regimes: Mo(PH3)5H2. J Phys Chem A 2022; 126:6834-6848. [PMID: 36154020 DOI: 10.1021/acs.jpca.2c03397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The transition-metal complex Mo(PH3)5H2 is known to exist in three possible isomeric forms, including a nonclassical, σ-bound dihydrogen complex and two classical dihydride isomers. As such, it has served as a model complex for the energies of conversion between these limiting structural regimes. In the present study, ab initio molecular dynamics computer simulations, combined with enhanced sampling techniques, were utilized to directly assess the degree of motion and isomerization of the dihydrogen/dihydride moieties in this complex. Ligand rotations (for both the H2 unit and the phosphine units) were found to be dominant in the low-temperature (298 K) regime, and the classical thermodynamic distribution showed no probability of thermally accessing dihydride forms, although unrestrained molecular dynamics trajectories showed fleeting configurations outside of the σ-H2 configuration. Simulations at higher temperatures surprisingly revealed new tri-hydride isomers that are energetically competitive with the σ-H2 and cis-/trans-dihydride isomers. Low-energy pathways to hydrogen/hydride transfer and phosphine dissociation were readily accessible, which considerably expands the known isomeric flexibility of this complex.
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Affiliation(s)
- Diana L Reese
- Department of Chemistry and Biochemistry, Utah Tech University, 225 South University Avenue, St. George, Utah 84770, United States
| | - Ryan P Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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3
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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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4
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Gerber RB. My Trajectory in Molecular Reaction Dynamics and Spectroscopy. Annu Rev Phys Chem 2021; 72:1-34. [PMID: 33276702 DOI: 10.1146/annurev-physchem-090519-124238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This is the story of a career in theoretical chemistry during a time of dramatic changes in the field due to phenomenal growth in the availability of computational power. It is likewise the story of the highly gifted graduate students and postdoctoral fellows that I was fortunate to mentor throughout my career. It includes reminiscences of the great mentors that I had and of the exciting collaborations with both experimentalists and theorists on which I built much of my research. This is an account of the developments of exciting scientific disciplines in which I was involved: vibrational spectroscopy, molecular reaction mechanisms and dynamics, e.g., in atmospheric chemistry, and the prediction of new, exotic molecules, in particular noble gas molecules. From my very first project to my current work, my career in science has brought me the excitement and fascination of research. What a wonderful pursuit!
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Affiliation(s)
- Robert Benny Gerber
- The Fritz Haber Research Center and Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; .,Department of Chemistry, University of California, Irvine, California 92697, USA
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5
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Roy TK, Gerber RB. Dual Basis Approach for Ab Initio Anharmonic Calculations of Vibrational Spectroscopy: Application to Microsolvated Biomolecules. J Chem Theory Comput 2020; 16:7005-7016. [PMID: 32991804 DOI: 10.1021/acs.jctc.0c00725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A dual electronic basis set approach is introduced for more efficient but accurate calculations of the anharmonic vibrational spectra in the framework of the vibrational self-consistent field (VSCF) theory. In this approach, an accurate basis set is used to compute the vibrational spectra at the harmonic level. The results are used to scale the potential surface from a more modest but much more efficient basis set. The scaling is such that at the harmonic level the new, scaled potential agrees with one of the accurate basis sets. The approach is tested in the application of the microsolvated, protected amino acid Ac-Phe-OMe, using the scaled anharmonic hybrid potential in the VSCF and VSCF-PT2 algorithms. The hybrid potential method yields results that are in good accord with the experiment and very close to those obtained in calculations with the high-level, very costly potential from the large basis set. At the same time, the hybrid potential calculations are considerably less expensive. The results of the hybrid calculations are much more accurate than those computed from the potential surface corresponding to the modest basis set. The results are very encouraging for using the hybrid potential method for inexpensive yet sufficiently accurate anharmonic calculations for the spectra of large biomolecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Dist: Samba Jammu-181143, India
| | - R Benny Gerber
- Institute of Chemistry, The Hebrew University, Jerusalem 91904, Israel.,Department of Chemistry, University of California, Irvine, California 92697, United States
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6
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Klinting EL, Christiansen O, König C. Toward Accurate Theoretical Vibrational Spectra: A Case Study for Maleimide. J Phys Chem A 2020; 124:2616-2627. [DOI: 10.1021/acs.jpca.9b11915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Carolin König
- Institute of Physical Chemistry, Kiel University, Max-Eyth-Straße 1, D-24118 Kiel, Germany
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7
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Hassan I, Donati L, Stensitzki T, Keller BG, Heyne K, Imhof P. The vibrational spectrum of the hydrated alanine-leucine peptide in the amide region from IR experiments and first principles calculations. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.03.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Molina A, Smereka P, Zimmerman PM. Exploring the relationship between vibrational mode locality and coupling using constrained optimization. J Chem Phys 2016; 144:124111. [PMID: 27036431 DOI: 10.1063/1.4944743] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The use of alternate coordinate systems as a means to improve the efficiency and accuracy of anharmonic vibrational structure analysis has seen renewed interest in recent years. While normal modes (which diagonalize the mass-weighted Hessian matrix) are a typical choice, the delocalized nature of this basis makes it less optimal when anharmonicity is in play. When a set of modes is not designed to treat anharmonicity, anharmonic effects will contribute to inter-mode coupling in an uncontrolled fashion. These effects can be mitigated by introducing locality, but this comes at its own cost of potentially large second-order coupling terms. Herein, a method is described which partially localizes vibrations to connect the fully delocalized and fully localized limits. This allows a balance between the treatment of harmonic and anharmonic coupling, which minimizes the error that arises from neglected coupling terms. Partially localized modes are investigated for a range of model systems including a tetramer of hydrogen fluoride, water dimer, ethene, diphenylethane, and stilbene. Generally, partial localization reaches ∼75% of maximal locality while introducing less than ∼30% of the harmonic coupling of the fully localized system. Furthermore, partial localization produces mode pairs that are spatially separated and thus weakly coupled to one another. It is likely that this property can be exploited in the creation of model Hamiltonians that omit the coupling parameters of the distant (and therefore uncoupled) pairs.
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Affiliation(s)
- Andrew Molina
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Peter Smereka
- Department of Applied Mathematics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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9
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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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10
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Benoit DM. Vibrational Signature of a Single Water Molecule Adsorbed on Pt(111): Toward a Reliable Anharmonic Description. J Phys Chem A 2015; 119:11583-90. [PMID: 26535801 DOI: 10.1021/acs.jpca.5b08543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we present a thorough benchmarking of our direct anharmonic vibrational variation-perturbation approach for adsorbed molecules on surfaces. We then use our method to describe the vibrational structure of a water molecule adsorbed on a Pt(111) surface and compare our results with the available experimental data. By using an explicitly correlated hybrid method to describe the molecule-surface interaction, we improve on the initial periodic PBE/DZP potential energy landscape and obtain vibrational frequencies that are of near-experimental accuracy. We introduce an implementation of anharmonic z-polarized IR intensity calculation and explain the absence of antisymmetric O-H stretch in the experimental data for the adsorbed water molecule, while the symmetric O-H stretch is predicted to be visible.
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Affiliation(s)
- David M Benoit
- Department of Chemistry, University of Hull , Hull HU6 7RX, U.K
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11
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Fischer SA, Ueltschi TW, El-Khoury PZ, Mifflin AL, Hess WP, Wang HF, Cramer CJ, Govind N. Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The C-H Region of DMSO as a Case Study. J Phys Chem B 2015. [PMID: 26222601 DOI: 10.1021/acs.jpcb.5b03323] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical identification of hydrocarbons and in vibrational sum-frequency generation spectroscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a challenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide using a new ab initio molecular dynamics (AIMD) module that we have implemented in NWChem. Through a combination of AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Comprehensive anharmonic normal mode analysis of the C-H stretching region casts doubt upon previous experimental assignments of the shoulder on the symmetric C-H stretching peak. In addition, our AIMD simulations also show significant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.
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Affiliation(s)
- Sean A Fischer
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Tyler W Ueltschi
- Department of Chemistry, University of Puget Sound , 1500 North Warner Street, Tacoma, Washington 98416, United States
| | - Patrick Z El-Khoury
- Physical Sciences Division, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Amanda L Mifflin
- Department of Chemistry, University of Puget Sound , 1500 North Warner Street, Tacoma, Washington 98416, United States
| | - Wayne P Hess
- Physical Sciences Division, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Hong-Fei Wang
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Christopher J Cramer
- Department of Chemistry, Supercomputing Institute and Chemical Theory Center, University of Minnesota , 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
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12
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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: 87] [Impact Index Per Article: 9.7] [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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13
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König C, Christiansen O. Automatic determination of important mode–mode correlations in many-mode vibrational wave functions. J Chem Phys 2015; 142:144115. [DOI: 10.1063/1.4916518] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Carolin König
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus C, Denmark
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14
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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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15
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Roy TK, Carrington T, Gerber RB. Approximate first-principles anharmonic calculations of polyatomic spectra using MP2 and B3LYP potentials: comparisons with experiment. J Phys Chem A 2014; 118:6730-9. [PMID: 24977304 DOI: 10.1021/jp5060155] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.
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Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University , Jerusalem 91904, Israel
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16
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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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17
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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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18
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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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19
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Samsonyuk A, Scheurer C. Configuration space partitioning and matrix buildup scaling for the vibrational configuration interaction method. J Comput Chem 2012; 34:27-37. [DOI: 10.1002/jcc.23101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 07/29/2012] [Accepted: 08/05/2012] [Indexed: 11/10/2022]
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20
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Xie HB, Jin L, Rudić S, Simons JP, Gerber RB. Computational Studies of Protonated β-d-Galactose and Its Hydrated Complex: Structures, Interactions, Proton Transfer Dynamics, and Spectroscopy. J Phys Chem B 2012; 116:4851-9. [DOI: 10.1021/jp3028325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong-bin Xie
- Key Laboratory of Industrial
Ecology and Environmental Engineering (MOE), School of Environmental
Science and Technology, Dalian University of Technology, Dalian 116024, China
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Lin Jin
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
| | - Svemir Rudić
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - John P. Simons
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ,
U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697-2025,
United States
- Institute of Chemistry
and The
Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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21
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Biczysko M, Bloino J, Carnimeo I, Panek P, Barone V. Fully ab initio IR spectra for complex molecular systems from perturbative vibrational approaches: Glycine as a test case. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2011.10.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Jin L, Simons JP, Gerber RB. Structures of the xylose–water complex: Energetics, transitions between conformers and spectroscopy. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.11.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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23
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Pele L, Šebek J, Potma EO, Benny Gerber R. Raman and IR spectra of butane: Anharmonic calculations and interpretation of room temperature spectra. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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24
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Carnimeo I, Biczysko M, Bloino J, Barone V. Reliable structural, thermodynamic, and spectroscopic properties of organic molecules adsorbed on silicon surfaces from computational modeling: the case of glycine@Si(100). Phys Chem Chem Phys 2011; 13:16713-27. [PMID: 21858336 DOI: 10.1039/c1cp21636h] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chemisorption of glycine on Si(100) has been studied by an integrated computational strategy based on perturbative anharmonic computations employing geometries and harmonic force fields evaluated by hybrid density functionals coupled to purposely tailored basis sets. It is shown that such a strategy allows the prediction of spectroscopic properties of isolated and chemisorbed molecules with comparable accuracy, paving the route toward a detailed analysis of surface-induced changes of glycine vibrational spectra.
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Affiliation(s)
- Ivan Carnimeo
- Scuola Normale Superiore and INSTM M3-Village, Pisa, Italy
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25
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Martens SM, Marta RA, Martens JK, McMahon TB. Tridentate Ionic Hydrogen-Bonding Interactions of the 5-Fluorocytosine Cationic Dimer and Other 5-Fluorocytosine Analogues Characterized by IRMPD Spectroscopy and Electronic Structure Calculations. J Phys Chem A 2011; 115:9837-44. [DOI: 10.1021/jp201513j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sabrina M. Martens
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Rick A. Marta
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Jonathan K. Martens
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
| | - Terry B. McMahon
- Department of Chemistry, University of Waterloo, 200 University Avenue, Waterloo, Ontario N2L 3G1, Canada
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26
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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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27
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Shmilovits-Ofir M, Miller Y, Gerber RB. Conformational transitions of glycine induced by vibrational excitation of the O-H stretch. Phys Chem Chem Phys 2011; 13:8715-22. [PMID: 20922237 DOI: 10.1039/c0cp01385d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational energy flow and conformational transitions following excitation of the OH stretching mode of the most stable conformer of glycine are studied by classical trajectories. "On the fly" simulations with the PM3 semiempirical electronic structure method for the potential surface are used. Initial conditions are selected to correspond to the ν=1 excitation of the OH stretch. The main findings are: (1) An an equilibrium-like ratio is established between the populations of the 3 lowest-lying conformers after about 10 picoseconds. (2) There is a high probability throughout the 150 ps of the simulations for finding the molecule in geometries far from the equilibrium structures of the lowest-energy conformers. (3) Energy from the initial excited OH (ν=1) stretch flows preferentially to 5 other vibrational modes, including the bending motion of the H atom. (4) RRK theory yields conformational transition rates that deviate substantially from the classical trajectory results. Possible implication of these results for vibrational energy flow and conformational transitions in small biological molecules are discussed.
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Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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28
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Goldstein M, Fredj E, Gerber RB. A new hybrid algorithm for finding the lowest minima of potential surfaces: Approach and application to peptides. J Comput Chem 2011; 32:1785-800. [DOI: 10.1002/jcc.21755] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 11/13/2010] [Accepted: 12/18/2010] [Indexed: 11/11/2022]
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29
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Brauer B, Pincu M, Buch V, Bar I, Simons JP, Gerber RB. Vibrational Spectra of α-Glucose, β-Glucose, and Sucrose: Anharmonic Calculations and Experiment. J Phys Chem A 2011; 115:5859-72. [DOI: 10.1021/jp110043k] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Victoria Buch
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - John. P. Simons
- Chemistry Department, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford, OX1 3QZ, U.K
| | - R. Benny Gerber
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697, United States
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30
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Meng K, Wang J. Anharmonic overtone and combination states of glycine and two model peptides examined by vibrational self-consistent field theory. Phys Chem Chem Phys 2011; 13:2001-13. [DOI: 10.1039/c0cp01177k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Kowal AT. Ab initio molecular geometry and anharmonic vibrational spectra of thiourea and thiourea-d4. J Comput Chem 2010; 32:718-29. [DOI: 10.1002/jcc.21665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 07/07/2010] [Accepted: 08/07/2010] [Indexed: 11/10/2022]
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32
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Suwan I, Gerber R. VSCF in internal coordinates and the calculation of anharmonic torsional mode transitions. Chem Phys 2010. [DOI: 10.1016/j.chemphys.2010.05.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Seidler P, Christiansen O. Automatic derivation and evaluation of vibrational coupled cluster theory equations. J Chem Phys 2009; 131:234109. [DOI: 10.1063/1.3272796] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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34
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Seidler P, Kaga T, Yagi K, Christiansen O, Hirao K. On the coupling strength in potential energy surfaces for vibrational calculations. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.10.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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35
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Benoit DM. Fast vibrational calculation of anharmonic OH-stretch frequencies for two low-energy noradrenaline conformers. J Chem Phys 2008; 129:234304. [DOI: 10.1063/1.3040427] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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36
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Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(100)-2×1 surface. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Bounouar M, Scheurer C. The impact of approximate VSCF schemes and curvilinear coordinates on the anharmonic vibrational frequencies of formamide and thioformamide. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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38
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Pele L, Gerber RB. On the number of significant mode-mode anharmonic couplings in vibrational calculations: Correlation-corrected vibrational self-consistent field treatment of di-, tri-, and tetrapeptides. J Chem Phys 2008; 128:165105. [DOI: 10.1063/1.2909558] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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39
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Miller Y, Chaban GM, Zhou J, Asmis KR, Neumark DM, Gerber RB. Vibrational spectroscopy of (SO42−)∙(H2O)n clusters, n=1–5: Harmonic and anharmonic calculations and experiment. J Chem Phys 2007; 127:094305. [PMID: 17824737 DOI: 10.1063/1.2764074] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The vibrational spectroscopy of (SO4(2-)).(H2O)n is studied by theoretical calculations for n=1-5, and the results are compared with experiments for n=3-5. The calculations use both ab initio MP2 and DFT/B3LYP potential energy surfaces. Both harmonic and anharmonic calculations are reported, the latter with the CC-VSCF method. The main findings are the following: (1) With one exception (H2O bending mode), the anharmonicity of the observed transitions, all in the experimental window of 540-1850 cm(-1), is negligible. The computed anharmonic coupling suggests that intramolecular vibrational redistribution does not play any role for the observed linewidths. (2) Comparison with experiment at the harmonic level of computed fundamental frequencies indicates that MP2 is significantly more accurate than DFT/B3LYP for these systems. (3) Strong anharmonic effects are, however, calculated for numerous transitions of these systems, which are outside the present observation window. These include fundamentals as well as combination modes. (4) Combination modes for the n=1 and n=2 clusters are computed. Several relatively strong combination transitions are predicted. These show strong anharmonic effects. (5) An interesting effect of the zero point energy (ZPE) on structure is found for (SO4(2-)).(H2O)(5): The global minimum of the potential energy corresponds to a C(s) structure, but with incorporation of ZPE the lowest energy structure is C2v, in accordance with experiment. (6) No stable structures were found for (OH-).(HSO4-).(H2O)n, for n<or=5.
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Affiliation(s)
- Yifat Miller
- Department of Physical Chemistry, The Hebrew University, Jerusalem 91904, Israel
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40
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Abstract
Gas-phase spectroscopy lends itself ideally to the study of isolated molecules and provides important data for comparison with theory. In recent years, we have seen enormous progress in the study of biomolecular building blocks in the gas phase. The motivation for such work is threefold: (a) It is important to distinguish between intrinsic molecular properties and properties that result from the biological environment. (b) Gas-phase spectroscopy of clusters provides insights into fundamental interactions and into microsolvation. (c) Gas-phase data support quantum-chemical calculations. This review focuses on the current status of (poly)amino acids and DNA bases. Recent results help elucidate structure and hydrogen-bonded interactions, as well as showcase a successful interplay between theory and experiment.
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Affiliation(s)
- Mattanjah S de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA.
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41
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Christiansen O. Vibrational structure theory: new vibrational wave function methods for calculation of anharmonic vibrational energies and vibrational contributions to molecular properties. Phys Chem Chem Phys 2007; 9:2942-53. [PMID: 17551617 DOI: 10.1039/b618764a] [Citation(s) in RCA: 190] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of recently developed theoretical methods for the calculation of vibrational energies and wave functions are reviewed. Methods for constructing the appropriate quantum mechanical Hamilton operator are briefly described before reviewing a particular branch of theoretical methods for solving the nuclear Schrödinger equation. The main focus is on wave function methods using the vibrational self-consistent field (VSCF) as starting point, and includes vibrational configuration interaction (VCI), vibrational Møller-Plesset (VMP) theory, and vibrational coupled cluster (VCC) theory. The convergence of the different methods towards the full vibrational configuration interaction (FVCI) result is discussed. Finally, newly developed vibrational response methods for calculation of vibrational contributions to properties, energies, and transition probabilities are discussed.
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Affiliation(s)
- Ove Christiansen
- The Lundbeck Foundation Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, DK-8000 Arhus C, Denmark
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42
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Ramaekers R, Pajak J, Lambie B, Maes G. Neutral and zwitterionic glycine.H(2)O complexes: A theoretical and matrix-isolation Fourier transform infrared study. J Chem Phys 2006; 120:4182-93. [PMID: 15268585 DOI: 10.1063/1.1643735] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The H-bond interaction between glycine and H2O has been studied by a combined theoretical (DFT(B3LYP)/6-31++G(**)) and experimental (matrix-isolation FT-IR) methodology. The 1:1 and 1:2 complexes of the most stable conformation (I) of glycine appear to be neutral complexes which have been vibrationally characterized in detail. The higher stoichiometry complexes (glycine).(H2O)n with n larger than 3 are demonstrated to be zwitterionic H-bonded complexes. A set of characteristic IR absorption bands for this zwitterionic structure has been observed in low-temperature Ar matrices. This would be the first experimental IR evidence for proton transfer occurring between the NH2 and COOH groups of amino acids by a H-bonded water molecular channel in isolated conditions.
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Affiliation(s)
- Riet Ramaekers
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Leuven, Belgium
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43
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Abstract
A new formalism for calculating and analyzing many-mode quantum dynamics is presented. The formalism is similar in spirit to the second quantization formulation of electronic structure theory. The similarity means that similar techniques can be employed for calculating the many-mode nuclear wave function. As a consequence a new formulation of the vibrational self-consistent-field (VSCF) method can be developed. Another result is that the formalism opens up for the construction of new methods that go beyond the VSCF level. A vibrational coupled cluster (VCC) theory is constructed using the new formalism. The size-extensivity concept is introduced in the context of multimode wave functions and the size extensivity of approximate VCC methods is illustrated in comparison with the non-size-extensive vibrational configuration interaction method.
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Affiliation(s)
- Ove Christiansen
- Department of Chemistry, University of Arhus, DK-8000 Arhus C, Denmark
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44
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Kowal AT. First-principles computation of the anharmonic vibrational spectra of sulfuryl halides SO2X2 (X=F, Cl, Br). Chem Phys 2006. [DOI: 10.1016/j.chemphys.2005.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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45
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Kowal AT. First-principles calculation of geometry and anharmonic vibrational spectra of thioformamide and thioformamide-d2. J Chem Phys 2006; 124:14304. [PMID: 16409033 DOI: 10.1063/1.2139995] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The equilibrium geometry of thioformamide HCSNH2 has been determined at the MP2 and CCSD(T) electron correlation levels under C(s) symmetry constraints using triple-zeta basis sets up to cc-pVTZ. All optimized planar structures are true minima on the potential-energy surface and are characterized by the C-N bond length within 1.353-1.343 A, C-S distances of 1.656-1.628 A, and NCS angle between 125.7 degrees and 125.9 degrees . The wave number of the NH2 out-of-plane wagging mode computed in the harmonic approximation shows stronger dependence on the basis set rather than the electron correlation level and varies from 85.9 cm(-1) at CCSD(T)cc-pVDZ level to 335 cm(-1) at MP2/aug-cc-pVTZ level. Anharmonic vibrational spectra of HCSNH2 and HCSND2 have been determined directly from the potential-energy surfaces computed at MP2 level in triple-zeta valence (TZV)(2df,2p) and TZV+(2df,2p) basis sets using vibrational self-consistent-field (VSCF) and correlation-corrected VSCF (CC-VSCF) methods. CC-VSCF wave numbers of fundamental, first overtone, and most intense combination transitions are reported for thioformamide and those of fundamentals for thioformamide-d2. The NH2 wagging (nu12) mode is strongly anharmonic and its fundamentals have been computed at 406.9 cm(-1) [TZV(2df,2p)] and 399.5 cm(-1) [TZV+(2df,2p)], which is remarkably close to the experimental energy of 393 cm(-1). Anharmonically computed fundamentals of this mode in thioformamide-d2, 299.7 cm(-1) [TZV(2df,2p)] and 299.6 cm(-1) [TZV+(2df,2p)], are only approximately 7 cm(-1) higher than the transition energy (293 cm(-1)) observed in the gas phase spectrum of HCSND2. The first overtone of the NH2 wagging mode of thioformamide (nu12 (02)) has been calculated by CC-VSCF procedure at 830.8 cm(-1) [TZV(2df,2p)] and 880.0 cm(-1) [TZV+(2df,2p)], which implies "negative" (nu12 (02)>2*nu12 (01)) anharmonicity of this mode.
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Affiliation(s)
- Andrzej T Kowal
- Department of Chemistry, Wrocław University of Technology, Wyb. St. Wyspiańskiego 27, 50-370 Wrocław, Poland.
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46
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Miller Y, Chaban GM, Gerber RB. Ab Initio Vibrational Calculations for H2SO4 and H2SO4·H2O: Spectroscopy and the Nature of the Anharmonic Couplings. J Phys Chem A 2005; 109:6565-74. [PMID: 16834003 DOI: 10.1021/jp058110l] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Vibrational frequencies for fundamental, overtone, and combination excitations of sulfuric acid (H2SO4) and of sulfuric acid monohydrate cluster (H2SO4 x H2O) are computed directly from ab initio MP2/TZP potential surface points using the correlation-corrected vibrational self-consistent field (CC-VSCF) method, which includes anharmonic effects. The results are compared with experiment. The computed transitions show in nearly all cases good agreement with experimental data and consistent improvement over the harmonic approximation. The CC-VSCF improvements over the harmonic approximation are largest for the overtone and combination excitations and for the OH stretching fundamental. The agreement between the calculations and experiment also supports the validity of the MP2/TZP potential surfaces. Anharmonic coupling between different vibrational modes is found to significantly affect the vibrational frequencies. Analysis of the mean magnitude of the anharmonic coupling interactions between different pairs of normal modes is carried out. The results suggest possible mechanisms for the internal flow of vibrational energy in H2SO4 and H2SO4 x H2O.
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Affiliation(s)
- Y Miller
- Department of Physical Chemistry and Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
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47
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Shemesh D, Gerber RB. Different chemical dynamics for different conformers of biological molecules: Photoionization of glycine. J Chem Phys 2005; 122:241104. [PMID: 16035739 DOI: 10.1063/1.1937407] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-photon ionization dynamics of two conformers of glycine is studied by classical trajectory simulations using the semiempirical PM3 potential surface in "on the fly" calculations. Initial conditions for the trajectories are weighted according to the Wigner distribution function computed for the initial vibrational ground state. Vertical ionization in the spirit of the classical Franck-Condon principle is assumed. The dynamics of the two conformers are compared during the first 10 ps. The comparison shows very different dynamical behavior for the two conformers. In particular, the chemical fragmentation pathways differ in part. Also, one of the conformers gives much higher rates of conformational transitions, while the other conformer gives larger chemical fragmentation yields. The example shows significantly different chemical dynamics for two conformers close in energy and separated by a low barrier.
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Affiliation(s)
- D Shemesh
- Department of Physical Chemistry, The Hebrew University, Jerusalem, Israel
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48
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Miller TF, Clary DC, Meijer AJHM. Collision-induced conformational changes in glycine. J Chem Phys 2005; 122:244323. [PMID: 16035773 DOI: 10.1063/1.1927527] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present quantum dynamical calculations on the conformational changes of glycine in collisions with the He, Ne, and Ar rare-gas atoms. For two conformer interconversion processes (III-->I and IV-->I), we find that the probability of interconversion is dependent on several factors, including the energy of the collision, the angle at which the colliding atom approaches the glycine molecule, and the strength of the glycine-atom interaction. Furthermore, we show that attractive interactions between the colliding atom and the glycine molecule catalyze conformer interconversion at low collision energies. In previous infrared spectroscopy studies of glycine trapped in rare-gas matrices and helium clusters, conformer III has been consistently observed, but conformer IV has yet to be conclusively detected. Because of the calculated thermodynamic stability of conformer IV, its elusiveness has been attributed to the IV-->I conformer interconversion process. However, our calculations present little indication that IV-->I interconversion occurs more readily than III-->I interconversion. Although we cannot determine whether conformer IV interconverts during experimental Ne- and Ar-matrix depositions, our evidence suggests that the conformer should be present in helium droplets. Anharmonic vibrational frequency calculations illustrate that previous efforts to detect conformer IV may have been hindered by the overlap of its IR-absorption bands with those of other conformers. We propose that the redshifted symmetric -CH(2) stretch of conformer IV provides a means for its conclusive experimental detection.
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Affiliation(s)
- Thomas F Miller
- Department of Physical and Theoretical Chemistry, Oxford University, UK
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49
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Adesokan AA, Fredj E, Brown EC, Gerber * RB. Anharmonic vibrational frequency calculations of 5,6-dihydrouracil and its complex with water: testing improved semiempirical potentials for biological molecules. Mol Phys 2005. [DOI: 10.1080/00268970500105201] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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50
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Theoretical study of anharmonic vibrational spectra of HNO3, HNO3–H2O, HNO4: Fundamental, overtone and combination excitations. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.01.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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