1
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Palanisamy N, Banik S. An approximation to the vibrational coupled-cluster method for CH-stretching of large molecules: application to naphthalene and anthracene. Phys Chem Chem Phys 2023; 25:20076-20092. [PMID: 37462438 DOI: 10.1039/d3cp01313h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
We propose an approximation to the vibrational coupled-cluster method (VCCM) to describe the CH-stretching region of the vibrational spectrum of large molecules. The vibrational modes of a molecule are divided into two sets: the target set and the bath set. The target set includes the CH stretches and the modes that are strongly coupled with the CH stretches and/or involve strong Fermi resonances with a CH stretch fundamental. The rest of the modes are in the bath set. First, the effective harmonic oscillator (EHO) approximation is invoked for the whole system to obtain the zeroth-order frequencies and modified potentials. The effects of interaction between the bath set and the target sets are included in the modified potential from the EHO calculation. The VCCM equations are constructed with the modified potential from the EHO calculations and for the target set only. The transition energies and intensities are calculated using such a truncated VCCM approximation. The proposed method is applied to calculate the IR spectra of naphthalene and anthracene. The results with three different criteria for selecting the modes in the target set are compared with the experimental IR spectra.
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Affiliation(s)
- Nivedhitha Palanisamy
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India.
| | - Subrata Banik
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India.
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2
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Wang Q, Wang Z, Kamimoto T, Deguchi Y, Cao S, Wen D, Takahara D. Multi-species hydrocarbon measurement using TDLAS with a wide scanning range DFG laser. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120333. [PMID: 34536892 DOI: 10.1016/j.saa.2021.120333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Tunable diode laser absorption spectroscopy (TDLAS) is a widely used diagnostic technique due to its high sensitivity, fast response, low cost, and other merits. Hydrocarbon detection is a field of great interest in the application of tunable diode lasers as hydrocarbons are fundamental molecules in many industrial processes. Many tunable diode lasers are only suitable for single species detection due to the short scanning range and in real situations. However, different hydrocarbon species tend to exist simultaneously. Here we present a laser system based on the difference-frequency generation (DFG) method for simultaneous hydrocarbon mixtures detection. The direct absorption spectra of different hydrocarbons covering various groups (e.g., alkane, olefin, and aromatic) were measured. The measurements of the concentration dependence of absorbance for each molecule were carried out. The R2 values were larger than 0.997, which demonstrated the system can measure hydrocarbons covering different molecular classes accurately. The mixture components were identified using the independent component analysis and quantitative analysis was performed using the classical least-squares method. Future studies will focus on the validation of the system in actual processes.
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Affiliation(s)
- Qiming Wang
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan
| | - Zhenzhen Wang
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan; State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Takahiro Kamimoto
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan
| | - Yoshihiro Deguchi
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan; State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Shengli Cao
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan; School of Power and Energy Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Du Wen
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan; State Key Laboratory of Multiphase Flow in Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Daichi Takahara
- Graduate School of Advanced Technology and Science, Tokushima University, Tokushima 770-8501, Japan
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3
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Yadav S, Banik S, Prasad MD. Understanding of the C-H stretch region of infra-red spectroscopy: an analysis of the final state wavefunctions. Phys Chem Chem Phys 2021; 23:9176-9188. [PMID: 33885051 DOI: 10.1039/d0cp01157f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of the wavefunctions associated with the final states in the CH stretching region of several medium sized molecules is analysed. The number of optically bright transitions is much larger than the number of CH oscillators present in the molecule, and they are spread over a range of about 300 cm-1. Several of them are clustered together within about 5 cm-1 with near equal intensities. The final states of all these transitions are superpositions of multiple zeroth order states. In almost all of such superpositions, no single zeroth order state has more than 50% weight. Several multiquantum states, with three to four quanta of excitation dominate the final states, with the CH chromophore contributing only a small weightage. Thus the band structure of the CH stretch region is due to several optically bright transitions whose final states are superpositions of low frequency multiquantum states with the CH chromophore contributing only a small weight to make them spectroscopically active.
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Affiliation(s)
- Swati Yadav
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India.
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4
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Dvores MP, Çarçabal P, Maître P, Simons JP, Gerber RB. Gas phase dynamics, conformational transitions and spectroscopy of charged saccharides: the oxocarbenium ion, protonated anhydrogalactose and protonated methyl galactopyranoside. Phys Chem Chem Phys 2020; 22:4144-4157. [PMID: 32039431 DOI: 10.1039/c9cp06572e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protonated intermediates are postulated to be involved in the rate determining step of many sugar reactions. This paper presents a study of protonated sugar species, isolated in the gas phase, using a combination of infrared multiple photon dissociation (IRMPD) spectroscopy, classical ab initio molecular dynamics (AIMD) and quantum mechanical vibrational self-consistent field (VSCF) calculations. It provides a likely identification of the reactive intermediate oxocarbenium ion structure in a d-galactosyl system as well as the saccharide pyrolysis product anhydrogalactose (that suggests oxocarbenium ion stabilization), along with the spectrum of the protonated parent species: methyl d-galactopyranoside-H+. Its vibrational fingerprint indicates intramolecular proton sharing. Classical AIMD simulations for galactosyl oxocarbenium ions, conducted in the temperature range ∼300-350 K (using B3LYP potentials on-the-fly) reveal efficient transitions on the picosecond timescale. Multiple conformers are likely to exist under the experimental conditions and along with static VSCF calculations, they have facilitated the identification of the individual structural motifs of the galactosyl oxocarbenium ion and protonated anhydrogalactose ion conformers that contribute to the observed experimental spectra. These results demonstrate the power of experimental IRMPD spectroscopy combined with dynamics simulations and with computational spectroscopy at the anharmonic level to unravel conformer structures of protonated saccharides, and to provide information on their lifetimes.
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Affiliation(s)
- M P Dvores
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel.
| | - P Çarçabal
- Université Paris-Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405, Orsay, France
| | - P Maître
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, 91405, Orsay, France
| | - J P Simons
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, Oxford University, South Parks Road, Oxford OX1 3QZ, UK
| | - R B Gerber
- Institute of Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel. and Department of Chemistry, University of California Irvine, CA 92697, USA
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5
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Shao M, Hu C, Sun J, Xu S, Xiang M, Zhu Q. Correlating Oxygen Species with Product Selectivity for Dehydrogenation of Butane over Titanium Mixed Oxide Catalysts. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b04938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingyuan Shao
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoquan Hu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiahan Sun
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuanghao Xu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Maoqiao Xiang
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingshan Zhu
- State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Bernath PF, Bittner DM, Sibert Iii EL. Isobutane Infrared Bands: Partial Rotational Assignments, ab Initio Calculations, and Local Mode Analysis. J Phys Chem A 2019; 123:6185-6193. [PMID: 31251627 DOI: 10.1021/acs.jpca.9b03321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-resolution infrared spectra of the symmetric top isobutane CH(CH3)3 were assigned with the help of ab initio calculations. The strong parallel band ν5(a1) with an origin at 1396.54741(76) cm-1 and the ν4(a1) mode, the CH2 scissors, at 1478.20363(41) cm-1 were rotationally analyzed. The bands in the C-H stretching region were assigned with the help of an anharmonic calculation and a local mode analysis.
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Affiliation(s)
- Peter F Bernath
- Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , Virginia 23529 , United States
| | - Dror M Bittner
- Department of Chemistry and Biochemistry , Old Dominion University , Norfolk , Virginia 23529 , United States
| | - Edwin L Sibert Iii
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
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7
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Wang S. Efficiently Calculating Anharmonic Frequencies of Molecular Vibration by Molecular Dynamics Trajectory Analysis. ACS OMEGA 2019; 4:9271-9283. [PMID: 31460016 PMCID: PMC6648323 DOI: 10.1021/acsomega.8b03364] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 05/13/2019] [Indexed: 05/28/2023]
Abstract
Two efficient methods, the Eckart frame algorithm and the multiorder derivative algorithm, for vibrational frequency calculation directly based on the raw data of atomic trajectory from the state-of-the-art first-principles molecular dynamics simulation are presented. The Eckart frame approach is robust to retrieve the full set of anharmonic fundamental frequencies of any molecule from the atomic trajectory for a sufficiently long molecular dynamics simulation at a temperature close to 0 K. In addition to the fundamental vibrational frequencies, the multiorder derivative approach is universal for the calculations of vibrational frequencies based on the molecular dynamics result in a wide range of temperatures. The accuracy, efficiency, and applicability of these two methods are demonstrated through several successful examples in calculating the anharmonic fundamental vibrational frequencies of methane, ethylene, water, and cyclobutadiene.
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8
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Roy TK, Kopysov V, Pereverzev A, Šebek J, Gerber RB, Boyarkin OV. Intrinsic structure of pentapeptide Leu-enkephalin: geometry optimization and validation by comparison of VSCF-PT2 calculations with cold ion spectroscopy. Phys Chem Chem Phys 2018; 20:24894-24901. [PMID: 30234204 DOI: 10.1039/c8cp03989e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The intrinsic structure of an opioid peptide [Ala2, Leu5]-leucine enkephalin (ALE) has been investigated using first-principles based vibrational self-consistent field (VSCF) theory and cold ion spectroscopy. IR-UV double resonance spectroscopy revealed the presence of only one highly abundant conformer of the singly protonated ALE, isolated and cryogenically cooled in the gas phase. High-level quantum mechanical calculations of electronic structures in conjunction with a systematic conformational search allowed for finding a few low-energy candidate structures. In order to identify the observed structure, we computed vibrational spectra of the candidate structures and employed the theory at the semi-empirically scaled harmonic level and at the first-principles based anharmonic VSCF levels. The best match between the calculated "anharmonic" and the measured spectra appeared, indeed, for the most stable candidate. An average of two spectra calculated with different quantum mechanical potentials is proposed for the best match with experiment. The match thus validates the calculated intrinsic structure of ALE and demonstrates the predictive power of first-principles theory for solving structures of such large molecules.
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Affiliation(s)
- Tapta Kanchan Roy
- Department of Chemistry and Chemical Sciences, Central University of Jammu, Rahya-Suchani (Bagla), Jammu 181143, India
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9
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Atakan A, Erdtman E, Mäkie P, Ojamäe L, Odén M. Time evolution of the CO2 hydrogenation to fuels over Cu-Zr-SBA-15 catalysts. J Catal 2018. [DOI: 10.1016/j.jcat.2018.03.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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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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11
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Vidal-Vidal Á, Pérez-Rodríguez M, Piñeiro MM. Direct transition mechanism for molecular diffusion in gas hydrates. RSC Adv 2016. [DOI: 10.1039/c5ra17867c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In this work, we use dual cage explicit atomic systems to demonstrate theoretically that direct transitions are feasible through hexagonal and pentagonal faces in type I hydrate without compromising the overall structure integrity.
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Affiliation(s)
- Á. Vidal-Vidal
- Departamento de Física Aplicada
- Universidade de Vigo
- Spain
| | | | - M. M. Piñeiro
- Departamento de Física Aplicada
- Universidade de Vigo
- Spain
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12
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Alam MJ, Ahmad S. FTIR, FT-Raman, UV-Visible spectra and quantum chemical calculations of allantoin molecule and its hydrogen bonded dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:961-978. [PMID: 25459622 DOI: 10.1016/j.saa.2014.09.119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/22/2014] [Accepted: 09/25/2014] [Indexed: 06/04/2023]
Abstract
FTIR, FT-Raman and electronic spectra of allantoin molecule are recorded and investigated using DFT and MP2 methods with 6-311++G(d,p) basis set. The molecular structure, anharmonic vibrational spectra, natural atomic charges, non-linear optical properties, etc. have been computed for the ground state of allantoin. The anharmonic vibrational frequencies are calculated using PT2 algorithm (Barone method) as well as VSCF and CC-VSCF methods. These methods yield results that are in remarkable agreement with the experiment. The coupling strengths between pairs of modes are also calculated using coupling integral based on 2MR-QFF approximation. The simulations on allantoin dimers have been also performed at B3LYP/6-311++G(d,p) level of theory to investigate the effect of the intermolecular interactions on the molecular structure and vibrational frequencies of the monomer. Vibrational assignments are made with the great accuracy using PED calculations and animated modes. The combination and overtone bands have been also identified in the FTIR spectrum with the help of anharmonic computations. The electronic spectra are simulated in gas and solution at TD-B3LYP/6-311++G(d,p) level of theory. The important global quantities such as electro-negativity, electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO, LUMO energy eigenvalues are also computed. NBO analysis has been performed for monomer and dimers of allantoin at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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13
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Vidal-Vidal Á, Pérez-Rodríguez M, Torré JP, Piñeiro MM. DFT calculation of the potential energy landscape topology and Raman spectra of type I CH4and CO2hydrates. Phys Chem Chem Phys 2015; 17:6963-75. [DOI: 10.1039/c4cp04962d] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Type I methane and carbon dioxide hydrates analyzed using DFT calculations: Raman spectra and potential energy landscape.
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Affiliation(s)
| | | | - Jean-Philippe Torré
- UMR 5150 Laboratoire des Fluides Complexes et leurs Réservoirs
- Université de Pau et des Pays de l'Adour
- Pau Cedex 64013
- France
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14
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Li X, Liu M, Lee JP, Ding D, Bottomley LA, Park S, Liu M. An operando surface enhanced Raman spectroscopy (SERS) study of carbon deposition on SOFC anodes. Phys Chem Chem Phys 2015; 17:21112-9. [DOI: 10.1039/c4cp05176a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thermally robust SERS probes enable the study of coking kinetics on the nickel surface at early stages and at the Ni–YSZ interface.
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Affiliation(s)
- Xiaxi Li
- School of Materials Science and Engineering
- Center for Innovative Fuel Cell and Battery Technologies
- Georgia Institute of Technology
- Atlanta
- USA
| | - Mingfei Liu
- School of Materials Science and Engineering
- Center for Innovative Fuel Cell and Battery Technologies
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jung-pil Lee
- School of Materials Science and Engineering
- Center for Innovative Fuel Cell and Battery Technologies
- Georgia Institute of Technology
- Atlanta
- USA
| | - Dong Ding
- School of Materials Science and Engineering
- Center for Innovative Fuel Cell and Battery Technologies
- Georgia Institute of Technology
- Atlanta
- USA
| | | | - Soojin Park
- Interdisciplinary School of Green Energy
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Republic of Korea
| | - Meilin Liu
- School of Materials Science and Engineering
- Center for Innovative Fuel Cell and Battery Technologies
- Georgia Institute of Technology
- Atlanta
- USA
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15
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Alam MJ, Ahmad S. Quantum chemical and spectroscopic investigations of 3-methyladenine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 128:653-664. [PMID: 24704482 DOI: 10.1016/j.saa.2014.02.170] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 02/17/2014] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.
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Affiliation(s)
| | - Shabbir Ahmad
- Department of Physics, Aligarh Muslim University, Aligarh 202002, India.
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16
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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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17
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Computational Vibrational Spectroscopy of glycine in aqueous solution – Fundamental considerations towards feasible methodologies. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Barone V, Biczysko M, Bloino J. Fully anharmonic IR and Raman spectra of medium-size molecular systems: accuracy and interpretation. Phys Chem Chem Phys 2014; 16:1759-87. [PMID: 24346191 PMCID: PMC4604664 DOI: 10.1039/c3cp53413h] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Computation of full infrared (IR) and Raman spectra (including absolute intensities and transition energies) for medium- and large-sized molecular systems beyond the harmonic approximation is one of the most interesting challenges of contemporary computational chemistry. Contrary to common beliefs, low-order perturbation theory is able to deliver results of high accuracy (actually often better than those issuing from current direct dynamics approaches) provided that anharmonic resonances are properly managed. This perspective sketches the recent developments in our research group toward the development of a robust and user-friendly virtual spectrometer rooted in second-order vibrational perturbation theory (VPT2) and usable also by non-specialists essentially as a black-box procedure. Several examples are explicitly worked out in order to illustrate the features of our computational tool together with the most important ongoing developments.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, piazza dei Cavalieri 7, I-56126 Pisa, Italy.
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19
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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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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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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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Abstract
Optical imaging with spectroscopic vibrational contrast is a label-free solution for visualizing, identifying, and quantifying a wide range of biomolecular compounds in biological materials. Both linear and nonlinear vibrational microscopy techniques derive their imaging contrast from infrared active or Raman allowed molecular transitions, which provide a rich palette for interrogating chemical and structural details of the sample. Yet nonlinear optical methods, which include both second-order sum-frequency generation (SFG) and third-order coherent Raman scattering (CRS) techniques, offer several improved imaging capabilities over their linear precursors. Nonlinear vibrational microscopy features unprecedented vibrational imaging speeds, provides strategies for higher spatial resolution, and gives access to additional molecular parameters. These advances have turned vibrational microscopy into a premier tool for chemically dissecting live cells and tissues. This review discusses the molecular contrast of SFG and CRS microscopy and highlights several of the advanced imaging capabilities that have impacted biological and biomedical research.
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Affiliation(s)
- Chao-Yu Chung
- Department of Chemistry, University of California, Irvine, California 92697, USA
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Alam MJ, Ahmad S. Anharmonic vibrational studies of L-aspartic acid using HF and DFT calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:992-1004. [PMID: 22939282 DOI: 10.1016/j.saa.2012.07.135] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/20/2012] [Accepted: 07/26/2012] [Indexed: 06/01/2023]
Abstract
The experimental and theoretical studies on the structure, molecular properties and vibrational spectra of L-aspartic acid are presented. The molecular structure, harmonic and anharmonic vibrational frequencies, molecular properties, MEP mapping, NBO analysis and electronic spectra of L-aspartic acid have been reported. Computed geometrical parameters and anharmonic frequencies of fundamental, combination and overtone transitions were found in satisfactory agreement with the experimental data. The UV-Vis spectrum of present molecule has been recorded and the electronic properties such as HOMO and LUMO energies and few low lying excited states were carried out by using time dependent density functional theory (TD-DFT) approach. Natural Bond Orbital (NBO) analysis has been performed for analyzing charge delocalization throughout the molecule. Molecular electrostatic potential map has also been used for quantitative measure of the chemical activities of various sites of the molecule.
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Affiliation(s)
- Mohammad Jane Alam
- Department of Physics, Aligarh Muslim University, Aligarh 202 002, India
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