1
|
Ahmadi S. Hydrated electrons and cluster science. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
2
|
Senthooran R, Curnow OJ, Crittenden DL. Discrete Oligomers and Polymers of Chloride Monohydrate Can Form in Encapsulated Environments: Structures and Infrared Spectra of [Cl 4 (H 2 O) 4 ] 4- and {[Cl(H 2 O)] - } ∞. Chempluschem 2021; 86:1297-1306. [PMID: 34491631 DOI: 10.1002/cplu.202100342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
A discrete tetrachloride tetrahydrate cluster, [Cl4 (H2 O)4 ]4- , was obtained with a partially-fluorinated triaminocyclopropenium cation, [C3 (N(CH2 CF3 )2 )(NEt2 )(NPr2 )]+ . The cluster consists of a [Cl2 (H2 O)2 ]2- square with each Cl- coordinated by another H2 O bridged to another Cl- . A 1D polymer of chloride monohydrate, {[Cl(H2 O)]- }∞ , was obtained with [C3 (N(CH2 CF3 )2 )2 (NBuMe)]+ . The tetrameric and polymeric structures were found to be computationally-unstable in the gas phase which indicates that an encapsulated environment is essential for their isolation. DFT and DFTB calculations were carried out on gas-phase [Cl4 (H2 O)4 ]4- to assist the infrared assignments. Anharmonically-corrected B3LYP transition frequencies were in close agreement with experiment, but DFTB models were only appropriate for qualitative interpretation. Solid-state DFTB calculations allowed the vibrational modes to be assigned. The results found are consistent with "discrete" chloride hydrates.
Collapse
Affiliation(s)
- Rathiga Senthooran
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| |
Collapse
|
3
|
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!
Collapse
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
| |
Collapse
|
4
|
Wyshusek M, Reiss GJ, Frank W. The Triple Salt 2(C
7
H
9
N
4
O
2
)[MoOCl
4
(H
2
O)] ⋅ 2(C
7
H
9
N
4
O
2
)Cl ⋅ (H
17
O
8
)Cl Containing a
C
2
‐symmetrical Unbranched H
+
(H
2
O)
8
Zundel
type Species in a Framework Composed of Theophyllinium, Aquatetrachloridooxidomolybdate and Chloride Ions. Z Anorg Allg Chem 2021. [DOI: 10.1002/zaac.202100007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Maik Wyshusek
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
| | - Guido J. Reiss
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
| | - Walter Frank
- Institut für Anorganische Chemie und Strukturchemie Heinrich-Heine-Universität Düsseldorf Universitätsstr 1 40225 Düsseldorf Germany
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Senthooran R, Curnow OJ, Brenner T, Weiss R, Ferreras M, Crittenden DL. A Series of Discrete Dichloride Dihydrates: Characterisation and Symmetry Effects. Chempluschem 2020; 85:2272-2280. [PMID: 32897648 DOI: 10.1002/cplu.202000563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/16/2020] [Indexed: 11/07/2022]
Abstract
A series of three discrete dichloride dihydrates [Cl2 (H2 O)2 ]2- have been isolated with different triaminocyclopropenium (TAC) cations and with different crystallographic symmetries. The cluster exhibits D2h symmetry with the tris(dimethylamino)cyclopropenium cation [C3 (NMe2 )3 ]+ , C2h symmetry with the fluorinated cation [C3 (N(CH2 CF3 )2 )(NBu2 )2 ]+ (containing two 2,2,2-trifluoroethyl substituents) and C2v symmetry with the more fluorinated [C3 (N(CH2 CF3 )2 )2 (NBu2 )]+ cation. The effect of symmetry on the infrared spectra of the dichloride ion-pair clusters, as well as deuterated analogues, has been investigated. The D2h - and C2h -symmetric clusters each exhibit two stretching bands in the infrared at 3427 and 3368 cm-1 for D2h symmetry and 3444 and 3392 cm-1 for C2h symmetry, whereas the C2v -symmetric cluster exhibits three bands at 3475, 3426 and 3373 cm-1 . Computational studies were carried out on a [Cl2 (H2 O)2 ]2- cluster with C2v symmetry to aid the infrared band assignments.
Collapse
Affiliation(s)
- Rathiga Senthooran
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Thomas Brenner
- Institut für Organische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054, Erlangen, Germany
| | - Robert Weiss
- Institut für Organische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Henkestraße 42, 91054, Erlangen, Germany
| | - Manuel Ferreras
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| |
Collapse
|
7
|
Curnow OJ, Senthooran R. One water to bind a chloride-chloride ion pair: isolation of discrete [Cl 2(H 2O)] 2- in the solid state. Dalton Trans 2020; 49:9579-9582. [PMID: 32647843 DOI: 10.1039/d0dt02300k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A discrete dichloride ion pair in the form of a monohydrate, [Cl2(H2O)]2-, was isolated using the triaminocyclopropenium cation [C3(NHex2)(N(CH2CF3)2)2]+. Although this ion pair is calculated to be unstable in the gas phase, the ionic lattice and weak CH-Cl hydrogen bonds assist the stabilization of the cluster. The D2O and HDO isotopomers were also prepared and characterized.
Collapse
Affiliation(s)
- Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand.
| | | |
Collapse
|
8
|
Abdelbassit MS, Curnow OJ, Ferreras M, Crittenden DL. A Discrete Dichloride Tetrahydrate Trapped by a Cyclopropenium Cation: Structure and Spectroscopic Properties. Chempluschem 2020; 85:927-932. [PMID: 32401422 DOI: 10.1002/cplu.202000146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/12/2020] [Accepted: 04/14/2020] [Indexed: 11/11/2022]
Abstract
A discrete dichloride tetrahydrate cluster, [Cl2 (H2 O)4 ]2- , was obtained as a salt of the bis(diphenylamino)diethylamino cyclopropenium cation [C3 (NPh2 )2 (NEt2 )]+ and characterized by single-crystal X-ray diffraction and infrared spectroscopy. This chloride-chloride ion-pair cluster consists of a [Cl2 (H2 O)2 ]2- square with opposite edges bridged by water molecules to give a chair-like structure of the non-hydrogen atoms. The solid-state structure is essentially the same as the calculated gas-phase structure. Infrared spectra were also collected on the deuterium analogue [Cl2 (D2 O)4 ]2- . Computational studies were carried out on gas-phase [Cl2 (H2 O)4 ]2- to confirm the infrared band assignments in the solid state. The structure and infrared spectrum are consistent with the discrete nature of the cluster.
Collapse
Affiliation(s)
- Mohammed S Abdelbassit
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Owen J Curnow
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Manuel Ferreras
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| | - Deborah L Crittenden
- School of Physical and Chemical Sciences, University of Canterbury, Private Bag, 4800, Christchurch, New Zealand
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Vibrational spectrum of HXeSH revisited: Combined computational and experimental study. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.137083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
11
|
Calculation of anharmonic effects for the unimolecular dissociation of CF3XCF2CH3 (X = Cl, Br) and CF3XCF2CD3 (X = Cl, Br). Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.136826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
12
|
Samala NR, Agmon N. Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters. J Phys Chem B 2019; 123:9428-9442. [PMID: 31553613 DOI: 10.1021/acs.jpcb.9b07777] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature (T) dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures. From a practical point of view, we find that NQE can be accounted for simply by subtracting a constant from the frequencies obtained from the velocity autocorrelation functions (VACF) of classical nuclear dynamics, resulting in unprecedented agreement with experiment, mostly within 5 cm-1. We have performed classical simulations of (H2O)n clusters (n = 2-5) from 20 K and up to their melting temperature, calculating both all-atom and partial VACF, thus generating the temperature dependence of the vibrational frequencies (IR and Raman bands). Focusing on the hydrogen-bonded (HBed) OH stretch and HOH bend, we find opposing T dependencies. The HBed OH modes blue shift linearly with T, attributed to ring expansion rather than any specific conformational change. The lowest-frequency Raman concerted mode is predicted to show the largest such shift. In contrast, the HOH bend undergoes a red-shift, with the highest frequency concerted band undergoing the largest red-shift. These results can be explained by a coupled-oscillator model for n hydrogen atoms on a ring, constrained to move either tangentially (stretch) or perpendicularly (bend) to the ring. With increasing temperature and weakening of HBs, the intrinsic force constant increases (stretch) or remains constant (bend), while the nearest-neighbor coupling constant decreases, and this results in the interesting behavior revealed herein. T-dependent Raman studies are required for testing some of these predictions.
Collapse
Affiliation(s)
- Nagaprasad Reddy Samala
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| |
Collapse
|
13
|
Harabuchi Y, Tani R, De Silva N, Njegic B, Gordon MS, Taketsugu T. Anharmonic vibrational computations with a quartic force field for curvilinear coordinates. J Chem Phys 2019. [DOI: 10.1063/1.5096167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryosuke Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - Bosiljka Njegic
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| |
Collapse
|
14
|
Tan JA, Kuo JL. Multilevel Approach for Direct VSCF/VCI MULTIMODE Calculations with Applications to Large “Zundel” Cations. J Chem Theory Comput 2018; 14:6405-6416. [DOI: 10.1021/acs.jctc.8b00679] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jake A. Tan
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan (ROC)
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, No. 1 Roosevelt Road, Section 4, Taipei 10617, Taiwan (ROC)
| |
Collapse
|
15
|
Li Q, Yao L, Lin SH. Anharmonic effect of the unimolecular dissociation of Glycerol to Glycidol. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1142/s0219633618500402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The unimolecular dissociation rate constants of the dehydration of Glycerol to Glycidol were calculated at the MP2/6–311G(d,p) level using the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The anharmonic effect of the reactions was examined by comparing the rate constants at temperatures (700–3000[Formula: see text]K) of the canonical case and total energies (25654–53089[Formula: see text]cm[Formula: see text]) of the microcanonical system. The calculations showed that high temperatures are required for the reaction to proceed. As the temperatures and total energies increased, the rate of reactions increased. However, the growth rate of the unimolecular dissociation rate constants was high and slower both in the canonical and microcanonical systems. Comparative analysis showed that the anharmonic effect was most significant for the reaction [Formula: see text] and least significant for the reaction [Formula: see text]. The anharmonic effect became more significant as the temperatures and total energies increased. Compared with the microcanonical situation, the anharmonic effect of the canonical system was more pronounced.
Collapse
Affiliation(s)
- Qian Li
- School of Energy and Mechanical Engineering, Jiangxi University of Science and Technology, Nanchang 330013, P. R. China
| | - Li Yao
- School of Marine Engineering, Dalian Maritime University, Dalian 116026, P. R. China
| | - S. H. Lin
- Department of Applied Chemistry, National Chiao–Tung University, Hsin–chu 10764, Taiwan
| |
Collapse
|
16
|
Mallory JD, Mandelshtam VA. Nuclear Quantum Effects and Thermodynamic Properties for Small (H2O)1–21X– Clusters (X– = F–, Cl–, Br–, I–). J Phys Chem A 2018; 122:4167-4180. [DOI: 10.1021/acs.jpca.8b00917] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Joel D. Mallory
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | | |
Collapse
|
17
|
Yagi K, Thomsen B. Infrared Spectra of Protonated Water Clusters, H+(H2O)4, in Eigen and Zundel Forms Studied by Vibrational Quasi-Degenerate Perturbation Theory. J Phys Chem A 2017; 121:2386-2398. [DOI: 10.1021/acs.jpca.6b11189] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory and ‡iTHES, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Bo Thomsen
- Theoretical
Molecular Science Laboratory and ‡iTHES, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| |
Collapse
|
18
|
Pitsevich G, Malevich A, Kozlovskaya E, Mahnach E, Doroshenko I, Pogorelov V, Pettersson LGM, Sablinskas V, Balevicius V. MP4 Study of the Anharmonic Coupling of the Shared Proton Stretching Vibration of the Protonated Water Dimer in Equilibrium and Transition States. J Phys Chem A 2017; 121:2151-2165. [PMID: 28187260 DOI: 10.1021/acs.jpca.7b00536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structure and harmonic and anharmonic IR spectra of the protonated water dimer (PWD) were calculated in C1, C2, and Cs symmetry at the MP4/acc-pVTZ level of theory. We found that structure and IR spectra are practically identical in C2 and C1 symmetry, demonstrating that an equilibrium C1 configuration of the PWD is not realized. Anharmonic coupling of the shared proton stretching vibration with all other modes in the PWD in C2 and Cs symmetry was the focus of this investigation. For this purpose, 28 two-dimensional potential energy surfaces (2D PES) were built at the MP4/acc-pVTZ level of theory and the corresponding vibrational Schrödinger equations were solved using the DVR method. Differences in the coupling of the investigated mode with other modes in the C2 and Cs configurations, along with some factors that determine the red- or blue-shift of the stretching vibration frequency, were analyzed. We obtained a rather reasonable value of the stretching frequency of the bridging proton (1058.4 cm-1) unperturbed by Fermi resonance. The Fermi resonance between the fundamental vibration ν7 and the combined vibration ν2 + ν6 of the same symmetry was analyzed through anharmonic second-order perturbation theory calculations, as well as by 3D PES constructed using Q2, Q6, and Q7 as normal coordinates. A significant (up to 50%) transfer of intensity from the fundamental vibration to the combined one was found. We have estimated the frequency of the bridging proton stretching vibration in the Cs configuration of the PWD based on calculations of the intrinsic anharmonicity and anharmonic double modes interactions at the MP4/acc-pVTZ level of theory (1261 cm-1).
Collapse
Affiliation(s)
- G Pitsevich
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - A Malevich
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - E Kozlovskaya
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - E Mahnach
- Department of Physical Optics, Belarusian State University , Nezavisimosti ave., 4, 220030 Minsk, Belarus
| | - I Doroshenko
- Taras Shevchenko National University of Kyiv , Volodymyrska str., 64\13, 01601, Kyiv, Ukraine
| | - V Pogorelov
- Taras Shevchenko National University of Kyiv , Volodymyrska str., 64\13, 01601, Kyiv, Ukraine
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
| | - V Sablinskas
- Faculty of Physics, Vilnius University , Sauletekio al. 9-3, LT-10222 Vilnius, Lithuania
| | - V Balevicius
- Faculty of Physics, Vilnius University , Sauletekio al. 9-3, LT-10222 Vilnius, Lithuania
| |
Collapse
|
19
|
Partanen L, Hänninen V, Halonen L. Effects of Global and Local Anharmonicities on the Thermodynamic Properties of Sulfuric Acid Monohydrate. J Chem Theory Comput 2016; 12:5511-5524. [PMID: 27662456 DOI: 10.1021/acs.jctc.6b00683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use state-of-the-art electronic structure calculation methods and large basis sets to obtain reliable values for the thermodynamic properties of sulfuric acid monohydrate and study the effects of vibrational anharmonicity on these properties. We distinguish between two forms of vibrational anharmonicity: local anharmonicity, which refers to the anharmonicity of the vibrational modes of a given cluster conformer, and global anharmonicity, which originates from accounting for the presence of different conformers in the first place. In our most accurate approach, we solve the nuclear Schrödinger equation variationally for the intermolecular large-amplitude motions, thus quantum-mechanically accounting for the presence of higher-energy conformers for both reactants and products, while using the standard vibrational perturbational approach for the other vibrational modes. This results in a value of -11.0 kJ/mol for the reaction Gibbs free energy at 298.15 K. When standard vibrational perturbational approaches are employed, the effects of local anharmonicity depend heavily on the choice of the electronic structure calculation basis set. In fact, better results can often be achieved by combining a simple harmonic treatment for the vibrational partition function with a statistical mechanical accounting of global anharmonicity. Thus, we recommend that future studies that intend to include anharmonicity start by accounting for the presence of higher-energy conformers and only then consider whether local anharmonicity calculations are feasible and necessary.
Collapse
Affiliation(s)
- Lauri Partanen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki , P.O. Box 55, A.I. Virtasen aukio 1, FIN-00014 Helsinki, Finland
| | - Vesa Hänninen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki , P.O. Box 55, A.I. Virtasen aukio 1, FIN-00014 Helsinki, Finland
| | - Lauri Halonen
- Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki , P.O. Box 55, A.I. Virtasen aukio 1, FIN-00014 Helsinki, Finland
| |
Collapse
|
20
|
Monteiro JG, Barbosa AG. VSCF calculations for the intra- and intermolecular vibrational modes of the water dimer and its isotopologs. Chem Phys 2016. [DOI: 10.1016/j.chemphys.2016.09.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
21
|
Melnikov VV, Yurchenko SN, Tennyson J, Jensen P. Radiative cooling of H 3O + and its deuterated isotopologues. Phys Chem Chem Phys 2016; 18:26268-26274. [PMID: 27711706 PMCID: PMC5315019 DOI: 10.1039/c6cp04661d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/28/2016] [Indexed: 11/21/2022]
Abstract
In conjunction with ab initio potential energy and dipole moment surfaces for the electronic ground state, we have made a theoretical study of the radiative lifetimes for the hydronium ion H3O+ and its deuterated isotopologues. We compute the ro-vibrational energy levels and their associated wavefunctions together with Einstein coefficients for electric dipole transitions. A detailed analysis of the stability of the ro-vibrational states has been carried out and the longest-living states of the hydronium ions have been identified. We report estimated radiative lifetimes and cooling functions for temperatures <200 K. A number of long-living meta-stable states are identified, capable of population trapping.
Collapse
Affiliation(s)
- Vladlen V Melnikov
- Siberian Institute of Physics & Technology, Tomsk State University, Tomsk, 634050, Russia
| | - Sergei N Yurchenko
- Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Jonathan Tennyson
- Department of Physics & Astronomy, University College London, London WC1E 6BT, UK.
| | - Per Jensen
- Physikalische und Theoretische Chemie, Fakultät für Mathematik und Naturwissenschaften, Bergische Universität Wuppertal, 42097 Wuppertal, Germany
| |
Collapse
|
22
|
Chen W, Chen GH, Wu D, Wang Q. BNg3F3: the first three noble gas atoms inserted into mono-centric neutral compounds - a theoretical study. Phys Chem Chem Phys 2016; 18:17534-45. [PMID: 27301893 DOI: 10.1039/c6cp01432a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Following the study of HXeOXeH and HXeCCXeH, in which two Xe atoms were inserted into H2O and C2H2 theoretically and experimentally, the structures and stability of BNg3F3 (Ng = Ar, Kr and Xe), in which three Ng atoms are inserted into BF3, have been explored theoretically using DFT and ab initio calculations. It is shown that BNg3F3 (Ng = Ar, Kr and Xe) with D3h symmetry are local minima with short B-Ng bond lengths of 1.966, 2.027 and 2.214 Å at the CCSD(T)/aug-cc-pVTZ/LJ18 level, which are close to their covalent limits. Note that although BNg3F3 (Ng = Kr and Xe) are energetically higher than the dissociation products 3Ng + BF3, they are still kinetically stable as metastable species with protecting barriers of 13.38 and 17.99 kcal mol(-1) for BKr3F3 and BXe3F3. Moreover, BKr3F3, the tri-Kr-inserted compound, even has comparable kinetic stability to HXeOXeH and HXeOXeF. In addition, upon the formation of BNg3F3, there is a large amount of charge transferred from B to Ng of at least 0.619 e. The calculated Wiberg Bond Indices (WBI) suggest that B-Ng bonds are naturally singly bonded; the large vibrational frequencies of B-Ng and Ng-F stretching modes and the negative Laplacian electron density of B-Ng bonds confirm further that BNg3F3 are stiff molecules with covalent B-Ng bonds. It should be noted that three Ng atoms inserted into mono-centric neutral molecules have not been reported previously. We hope that the present theoretical study may provide important evidence for the experimental synthesis of BNg3F3.
Collapse
Affiliation(s)
- Wei Chen
- Department of Chemistry, Shantou University, Shantou 515063, China.
| | - Guang-Hui Chen
- Department of Chemistry, Shantou University, Shantou 515063, China.
| | - Di Wu
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Qiang Wang
- Department of Applied Chemistry, College of Science, Nanjing Tech University, Nanjing 211816, China
| |
Collapse
|
23
|
Li Q, Yao L, Lin S. Calculation of anharmonic effects for the unimolecular dissociation of CH 3OOH and its deuterated species CD 3OOD using the Rice–Ramsperger–Kassel–Marcus theory. CAN J CHEM 2015. [DOI: 10.1139/cjc-2015-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Anharmonic and harmonic rate constants for the unimolecular dissociation of CH3OOH and CD3OOD were calculated using the Rice–Ramsperger–Kassel–Marcus (RRKM) theory at the MP2/6-311++G(3df,3pd) level of theory. The anharmonic effect of the reactions was investigated. Comparison of results for the decompositions of CH3OOH and CD3OOD shows that the direct bond dissociation channel, CH3(D3) O + OH (D), is the most dominant reaction. The anharmonic effect plays an important role in the unimolecular dissociation of both CH3OOH and CD3OOD. For channels CH3(D3) O + OH (D) and CH3(D3) + H (D) O2, the anharmonic effect of the unimolecular dissociation of CD3OOD is more pronounced than that of the unimolecular dissociation of CH3OOH. For channel H2(D2) CO + H2(D2) O, the anharmonic effect of the unimolecular dissociation of CH3OOH is more pronounced than that of the unimolecular dissociation of CD3OOD. The isotope effect is more distinct in the anharmonic oscillator model.
Collapse
Affiliation(s)
- Qian Li
- School of Marine Engineering, Dalian Maritime University, Dalian 116026, China
| | - Li Yao
- School of Marine Engineering, Dalian Maritime University, Dalian 116026, China
| | - S.H. Lin
- Department of Applied Chemistry, National Chiao-Tung University, Hsin-chu, Taiwan, 10764
| |
Collapse
|
24
|
Li Q, Yao L, Lin SH. Anharmonic Effect of the Unimolecular Isomerization/Decomposition of Benzyne. J CHIN CHEM SOC-TAIP 2015. [DOI: 10.1002/jccs.201400345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
25
|
Kondati Natarajan S, Morawietz T, Behler J. Representing the potential-energy surface of protonated water clusters by high-dimensional neural network potentials. Phys Chem Chem Phys 2015; 17:8356-71. [DOI: 10.1039/c4cp04751f] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a reactive neural network potential for protonated water clusters that accurately represents the density-functional theory potential-energy surface.
Collapse
Affiliation(s)
| | - Tobias Morawietz
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
| | - Jörg Behler
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- D-44780 Bochum
- Germany
| |
Collapse
|
26
|
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.
Collapse
|
27
|
Rozenberg M, Loewenschuss A, Nielsen CJ. Hydrogen Bonding in the Sulfuric Acid–Methanol–Water System: A Matrix Isolation and Computational Study. J Phys Chem A 2014; 119:2271-80. [DOI: 10.1021/jp505965z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mark Rozenberg
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel 919040
| | - Aharon Loewenschuss
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel 919040
| | - Claus J. Nielsen
- Department
of Chemistry, University of Oslo, 1033 Blindern, N-0315 Oslo, Norway
| |
Collapse
|
28
|
Silva AF, Richter WE, Bruns RE. Quantum Theory of Atoms in Molecules/Charge–Charge Flux–Dipole Flux interpretation of fundamental vibrational intensity enhancements on H-bond formation of water trimer. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
29
|
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.
Collapse
Affiliation(s)
- Tapta Kanchan Roy
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University , Jerusalem 91904, Israel
| | | | | |
Collapse
|
30
|
|
31
|
Silva AF, Richter WE, Terrabuio LA, Haiduke RLA, Bruns RE. Quantum theory of atoms in molecules/charge-charge flux-dipole flux models for fundamental vibrational intensity changes on H-bond formation of water and hydrogen fluoride. J Chem Phys 2014; 140:084306. [DOI: 10.1063/1.4865938] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
32
|
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.
Collapse
Affiliation(s)
- Roie Knaanie
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | | | | | | |
Collapse
|
33
|
Beck JP, Cimas A, Lisy JM, Gaigeot MP. O-H anharmonic vibrational motions in Cl(-)···(CH3OH)(1-2) ionic clusters. Combined IRPD experiments and AIMD simulations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 119:12-17. [PMID: 23810567 DOI: 10.1016/j.saa.2013.05.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/19/2013] [Indexed: 06/02/2023]
Abstract
The structures of Cl(-)-(Methanol)1,2 clusters have been unraveled combining Infrared Predissociation (IR-PD) experiments and DFT-based molecular dynamics simulations (DFT-MD) at 100 K. The dynamical IR spectra extracted from DFT-MD provide the initial 600 cm(-1) large anharmonic red-shift of the O-H stretch from uncomplexed methanol (3682 cm(-1)) to Cl(-)-(Methanol)1 complex (3085 cm(-1)) as observed in the IR-PD experiment, as well as the subtle supplementary blue- and red-shifts of the O-H stretch in Cl(-)-(Methanol)2 depending on the structure. The anharmonic vibrational calculations remarkably provide the 100 cm(-1) O-H blue-shift when the two methanol molecules are simultaneously organized in the anion first hydration shell (conformer 2A), while they provide the 240 cm(-1) O-H red-shift when the second methanol is in the second hydration shell of Cl(-) (conformer 2B). RRKM calculations have also shown that 2A/2B conformers interconvert on a nanosecond time-scale at the estimated 100 K temperature of the clusters formed by evaporative cooling of argon prior to the IR-PD process.
Collapse
Affiliation(s)
- Jordan P Beck
- Concordia University Wisconsin, 12800 N. Lakeshore Drive, Mequon, WI 53097, USA.
| | | | | | | |
Collapse
|
34
|
Structure and thermodynamics of H3O+(H2O)8 clusters: A combined molecular dynamics and quantum mechanics approach. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
35
|
Miliordos E, Aprà E, Xantheas SS. Optimal geometries and harmonic vibrational frequencies of the global minima of water clusters (H2O)n, n = 2–6, and several hexamer local minima at the CCSD(T) level of theory. J Chem Phys 2013; 139:114302. [DOI: 10.1063/1.4820448] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
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
| |
Collapse
|
37
|
Song D, Su H, Kong FA, Lin SH. Anharmonic Rice-Ramsperger-Kassel-Marcus (RRKM) and product branching ratio calculations for the partially deuterated protonated water dimers: dissociation and isomerization. J Chem Phys 2013; 138:104301. [PMID: 23514483 DOI: 10.1063/1.4794152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Partially deuterated protonated water dimers, H2O·H(+)·D2O, H2O·D(+)·HDO, and HDO·H(+)·HDO, as important intermediates of isotopic labeled reaction of H3O(+) + D2O, undergo direct dissociation and indirect dissociation, i.e., isomerization before the dissociation. With Rice-Ramsperger-Kassel-Marcus theory and ab initio calculations, we have computed their dissociation and isomerization rate constants separately under the harmonic and anharmonic oscillator models. On the basis of the dissociation and isomerization rate constants, branching ratios of two primary products, [HD2O(+)]∕[H2DO(+)], are predicted under various kinetics models with the harmonic or anharmonic approximation included. The feasible kinetics model accounting for experimental results is shown to include anharmonic effect in describing dissociation, while adopting harmonic approximation for isomerization. Thus, the anharmonic effect is found to play important roles affecting the dissociation reaction, while isomerization rates are shown to be insensitive to whether the anharmonic or harmonic oscillator model is being applied.
Collapse
Affiliation(s)
- Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
| | | | | | | |
Collapse
|
38
|
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]
|
39
|
Pandey P, Chakraborty T. Doubly Hydrogen Bonded Dimer of δ-Valerolactam: Infrared Spectrum and Intermode Coupling. J Phys Chem A 2012; 116:8972-9. [DOI: 10.1021/jp307079k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Prasenjit Pandey
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur,
Kolkata 700032, India
| | - Tapas Chakraborty
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur,
Kolkata 700032, India
| |
Collapse
|
40
|
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]
|
41
|
Shmilovits-Ofir M, Gerber RB. Proton Transfer and Dissociation of GlyLysH+ following O–H and N–H Stretching Mode Excitations: Dynamics Simulations. J Am Chem Soc 2011; 133:16510-7. [DOI: 10.1021/ja205634b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michaela Shmilovits-Ofir
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - R. Benny Gerber
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| |
Collapse
|
42
|
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
| |
Collapse
|
43
|
Temelso B, Shields GC. The Role of Anharmonicity in Hydrogen-Bonded Systems: The Case of Water Clusters. J Chem Theory Comput 2011; 7:2804-17. [DOI: 10.1021/ct2003308] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Berhane Temelso
- Dean’s Office, College of Arts and Sciences, Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - George C. Shields
- Dean’s Office, College of Arts and Sciences, Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| |
Collapse
|
44
|
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.
Collapse
Affiliation(s)
- Jiří Šebek
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | | | | | | |
Collapse
|
45
|
Guasco TL, Johnson MA, McCoy AB. Unraveling Anharmonic Effects in the Vibrational Predissociation Spectra of H5O2+ and Its Deuterated Analogues. J Phys Chem A 2011; 115:5847-58. [DOI: 10.1021/jp109999b] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy L. Guasco
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Mark A. Johnson
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Anne B. McCoy
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
46
|
Ramos-Cordoba E, Lambrecht DS, Head-Gordon M. Charge-transfer and the hydrogen bond: Spectroscopic and structural implications from electronic structure calculations. Faraday Discuss 2011; 150:345-62; discussion 391-418. [DOI: 10.1039/c1fd00004g] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
47
|
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]
|
48
|
Callahan KM, Casillas-Ituarte NN, Xu M, Roeselová M, Allen HC, Tobias DJ. Effect of magnesium cation on the interfacial properties of aqueous salt solutions. J Phys Chem A 2010; 114:8359-68. [PMID: 20701343 DOI: 10.1021/jp103485t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sodium chloride solutions have been used extensively as a model of seawater in both theoretical and experimental studies of the chemistry of sea salt aerosol. Many groups have found that chloride anions are present at the air-solution interface. This observation has been important for the development of a mechanism for the heterogeneous production of molecular chlorine from chloride in sea salt aerosol. However, while sodium chloride is a major constituent of seawater, it is by no means the only salt present. Seawater contains one Mg(2+) for every eight Na(+). Mg(2+) is naturally occurring in ocean waters from mineral deposits in the Earth's crust and biological sources. Mg(2+) forms a hexahydrate structure, rather than contact ion pairs with chloride anion, and this impacts the ordering of water in solution. In this study, we use molecular dynamics simulations, ab initio calculations, and vibrational sum frequency generation (SFG) spectroscopy to explore the effect of the Mg(2+) cation and its tightly bound solvation shell on the surface propensity of chloride, ion-ion interactions, and water structure of the air-solution interface of concentrated chloride salt solutions. In addition, we provide molecular level details that may be relevant to the heterogeneous reactions of chloride in deliquesced sea salt aerosols. In particular, we show that the presence of the divalent Mg(2+) cation does not modify the surface propensity of chloride compared to Na(+) and hence, its availability to interfacial reaction, although some differences in the behavior of chloride may occur due to specific ion interactions. In this work, we also discuss the SFG free OH band at the surface of salt solutions and conclude that it is often not straightforward to interpret.
Collapse
Affiliation(s)
- Karen M Callahan
- AirUCI Environmental Molecular Science Institute and Department of Chemistry, University of California, Irvine, California 92697, USA
| | | | | | | | | | | |
Collapse
|
49
|
Xantheas SS. Anharmonic vibrational spectra of hydrogen bonded clusters: comparison between higher energy derivative and mean-field grid based methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350600922564] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Sotiris S. Xantheas
- a Chemical Sciences Division , Pacific Northwest National Laboratory , 902 Battelle Boulevard, PO Box 999, MS K1-83, Richland , WA, 99352 , USA
| |
Collapse
|
50
|
Rasheed T, Ahmad S. Approximate solution of the mode-mode coupling integral: Application to cytosine and its deuterated derivative. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:446-456. [PMID: 20638327 DOI: 10.1016/j.saa.2010.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 05/30/2010] [Accepted: 06/11/2010] [Indexed: 05/29/2023]
Abstract
Ab initio Hartree-Fock (HF), density functional theory (DFT) and second-order Møller-Plesset (MP2) methods were used to perform harmonic and anharmonic calculations for the biomolecule cytosine and its deuterated derivative. The anharmonic vibrational spectra were computed using the vibrational self-consistent field (VSCF) and correlation-corrected vibrational self-consistent field (CC-VSCF) methods. Calculated anharmonic frequencies have been compared with the argon matrix spectra reported in literature. The results were analyzed with focus on the properties of anharmonic couplings between pair of modes. A simple and easy to use formula for calculation of mode-mode coupling magnitudes has been derived. The key element in present approach is the approximation that only interactions between pairs of normal modes have been taken into account, while interactions of triples or more are neglected. FTIR and Raman spectra of solid state cytosine have been recorded in the regions 400-4000 cm(-1) and 60-4000 cm(-1), respectively. Vibrational analysis and assignments are based on calculated potential energy distribution (PED) values.
Collapse
Affiliation(s)
- Tabish Rasheed
- Department of Physics, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | | |
Collapse
|