scholarly journals The vibrational properties of benzene on an ordered water ice surface

2021 ◽  
Author(s):  
Victoria H J Clark ◽  
David M Benoit
Keyword(s):  
Gas Phase ◽  
Ir Spectrum ◽  
Density Functional ◽  
Hybrid Approach ◽  
Normal Modes ◽  
Intensity Pattern ◽  
Water Ice ◽  
Ice Surface ◽  
Vibrational Bands ◽  
Ordered Water

Abstract We present a hybrid CCSD(T)+PBE-D3 approach to calculating the vibrational signatures for gas phase benzene and benzene adsorbed on an ordered water-ice surface. We compare the results of our method against experimentally recorded spectra and calculations performed using PBE-D3-only approaches (harmonic and anharmonic). Calculations use a proton ordered XIh water-ice surface consisting of 288 water molecules, and results are compared against experimental spectra recorded for an ASW ice surface. We show the importance of including a water ice surface into spectroscopic calculations, owing to the resulting differences in vibrational modes, frequencies and intensities of transitions seen in the IR spectrum. The overall intensity pattern shifts from a dominating ν11 band in the gas-phase to several high-intensity carriers for an IR spectrum of adsorbed benzene. When used for adsorbed benzene, the hybrid approach presented here achieves an RMSD for IR active modes of 21 cm-1, compared to 72 cm-1 and 49 cm-1 for the anharmonic and harmonic PBE-D3 approaches, respectively. Our hybrid model for gaseous benzene also achieves the best results when compared to experiment, with an RMSD for IR active modes of 24 cm-1, compared to 55 cm-1 and 31 cm-1 for the anharmonic and harmonic PBE-D3 approaches, respectively. To facilitate assignment, we generate and provide a correspondence graph between the normal modes of the gaseous and adsorbed benzene molecules. Finally, we calculate the frequency shifts, Δν, of adsorbed benzene relative to its gas phase to highlight the effects of surface interactions on vibrational bands and evaluate the suitability of our chosen dispersion-corrected density functional theory.

Quantum chemical study on the formation of isopropyl cyanide and its linear isomer in the interstellar medium

2020 ◽  
pp. 1-11
Author(s):  
Keshav Kumar Singh ◽  
Poonam Tandon ◽  
Alka Misra ◽  
Shivani ◽  
Manisha Yadav ◽  
...  
Keyword(s):  
Amino Acids ◽  
Interstellar Medium ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Density Functional ◽  
Quantum Chemical Study ◽  
Chemical Study ◽  
Dark Cloud ◽  
Water Ice ◽  
Hydrocarbon Radicals

Abstract The formation mechanism of linear and isopropyl cyanide (hereafter n-PrCN and i-PrCN, respectively) in the interstellar medium (ISM) has been proposed from the reaction between some previously detected small cyanides/cyanide radicals and hydrocarbons/hydrocarbon radicals. n-PrCN and i-PrCN are nitriles therefore, they can be precursors of amino acids via Strecker synthesis. The chemistry of i-PrCN is especially important since it is the first and only branched molecule in ISM, hence, it could be a precursor of branched amino acids such as leucine, isoleucine, etc. Therefore, both n-PrCN and i-PrCN have significant astrobiological importance. To study the formation of n-PrCN and i-PrCN in ISM, quantum chemical calculations have been performed using density functional theory at the MP2/6-311++G(2d,p)//M062X/6-311+G(2d,p) level. All the proposed reactions have been studied in the gas phase and the interstellar water ice. It is found that reactions of small cyanide with hydrocarbon radicals result in the formation of either large cyanide radicals or ethyl and vinyl cyanide, both of which are very important prebiotic interstellar species. They subsequently react with the radicals CH2 and CH3 to yield n-PrCN and i-PrCN. The proposed reactions are efficient in the hot cores of SgrB2 (N) (where both n-PrCN and i-PrCN were detected) due to either being barrierless or due to the presence of a permeable entrance barrier. However, the formation of n-PrCN and i-PrCN from the ethyl and vinyl cyanide always has an entrance barrier impermeable in the dark cloud; therefore, our proposed pathways are inefficient in the deep regions of molecular clouds. It is also observed that ethyl and vinyl cyanide serve as direct precursors to n-PrCN and i-PrCN and their abundance in ISM is directly related to the abundance of both isomers of propyl cyanide in ISM. In all the cases, reactions in the ice have smaller barriers compared to their gas-phase counterparts.

The vibrational signatures of polyaromatic hydrocarbons on an ice surface

2019 ◽  
Vol 15 (S350) ◽  
pp. 468-470
Author(s):  
Victoria H.J. Clark ◽  
David M. Benoit
Keyword(s):  
Vibrational Spectra ◽  
Density Functional ◽  
Polyaromatic Hydrocarbons ◽  
Functional Theory ◽  
Water Ice ◽  
Aromatic Molecules ◽  
Ice Surface ◽  
Vibrational Anharmonicity ◽  
Potential Energy Landscape ◽  
Crystalline Water

AbstractWe use quantum chemical techniques to model the vibrational spectra of small aromatic molecules on a proton-ordered hexagonal crystalline water ice (XIh) model. We achieve a good agreement with experimental data by accounting for vibrational anharmonicity and correcting the potential energy landscape for known failures of density functional theory. A standard harmonic description of the vibrational spectra only leads to a broad qualitative agreement.

scholarly journals The quest of chirality in the interstellar medium

2020 ◽  
Vol 633 ◽  
pp. A49
Author(s):  
Y. Ellinger ◽  
F. Pauzat ◽  
A. Markovits ◽  
A. Allaire ◽  
J.-C. Guillemin
Keyword(s):  
Interstellar Medium ◽  
Gas Phase ◽  
Propylene Oxide ◽  
Density Functional ◽  
Energy Scale ◽  
Potential Candidate ◽  
Structural Constraints ◽  
Water Ice ◽  
Rotational Spectra ◽  
Complex Organic Molecule

Context. All but one complex organic molecule (COM) detected so far in the interstellar medium (ISM) are achiral; propylene oxide (c-C2H3O)-CH3 is the only exception to this. Finding other chiral species is a priority for astrobiology to progress in the understanding of the emergence of life. Whatever the conditions of their formation, i.e., gas phase or grain chemistry, the detection relies on rotational spectra. This means that, if adsorbed after formation in the gas phase or directly formed on the icy grains, these COMs must escape in the gas phase as free flyers to be detectable. Aims. Learning the lesson drawn from the only observation of a chiral compound and considering the structural constraints imposed to a molecule to be chiral, we look at what species could satisfy these conditions and be potential targets for a radio astronomy search in the ISM gas phase. Methods. This question was addressed by combining two complementary approaches that rely on density functional theory. The structure, energetics, and spectroscopic parameters of each potential candidate were determined using molecular calculations. The propensity for a molecule to remain trapped on the ice coating of the grains was evaluated by numerical simulations making use of a solid state periodic model. Results. Replacing the -CH3 group on rigid propylene oxide by -CN, -CCH, -NH2, -OH, or -HCO gives oxirane daughter molecules whose adsorption energies divide into two classes: below and above the adsorption energy of H2O on solid water-ice ~13.5 kcal mol−1. Conclusions. The best chiral candidate would be a rigid molecule for an easier determination of its radio spectra. This molecule would be composed of a central carbon linked to one hydrogen and three different chemical groups as simple as possible. If not the most stable isomer, this candidate should be as close as possible on the energy scale, possess a significant dipole moment, and be less strongly attached to the ice than H2O itself.

Theoretical and experimental studies of IR and NMR spectra of gem-2,2-diamino-4,4,6,6-tetraphenoxy-1,3,5-cyclo-triaza-λ5-phosphorine

2010 ◽  
Vol 75 (11) ◽  
pp. 1125-1138
Author(s):  
Lenka Dastychová ◽  
Dalibor Dastych ◽  
Pavel Kubáček ◽  
Milan Alberti
Keyword(s):  
Density Functional ◽  
Nmr Spectra ◽  
Experimental Studies ◽  
Normal Modes ◽  
Chemical Calculation ◽  
Functional Theory ◽  
Calculation Results ◽  
Vibrational Bands ◽  
First Time ◽  
C Nmr

The vibrational spectra of gem-2,2-diamino-4,4,6,6-tetraphenoxy-1,3,5-cyclo-triaza-λ5-phosphorine were studied using density functional theory. Selected vibrational bands were assigned to normal modes on the basis of DFT calculation with the ADF program package. The 1H and 13C NMR spectra, the higher order 31P, 31P{1Ham.(sel.)} and 31P{1Harom.(sel.)} NMR spectra were measured and the values of 1J(C,H), 2J(C,H) and 2J(PI,PII) were found. Nearly the complete spin system (ABB′M4X4X4′) for the symmetry C2 was simulated with the gNMR simulation program and the values of 2J(PI,Ham.), 4J(PII,Ham.), 4J(PII,Harom.), 6J(PI,Harom.) and 6J(PII,H′arom.) were determined for the first time. The experimental NMR data were also compared with quantum chemical calculation results.

Conformational stability, barriers to internal rotations, and normal coordinate analysis of acetone and its2H-isotopomers

2016 ◽  
Vol 94 (10) ◽  
pp. 818-826 ◽  
Author(s):  
Mahboobeh Gholamhoseinpour ◽  
Sayyed Faramarz Tayyari ◽  
Saeedreza Emamian
Keyword(s):  
Density Functional ◽  
Conformational Stability ◽  
Normal Modes ◽  
Normal Coordinate Analysis ◽  
Basis Set ◽  
Basis Sets ◽  
Potential Energy Distribution ◽  
Normal Coordinate ◽  
Functional Theory ◽  
Vibrational Bands

Molecular structure and vibrational spectra of acetone, acetone-d3, and acetone-d6were investigated by means of ab initio and density functional theory (DFT) calculations. The harmonic and anharmonic vibrational frequencies of the acetone isotopomers were calculated at the B3LYP (using the 6–311++G(3df,3pd) basis set) and B2PLYP (using the 6–31+(2d,p) and 6–311G(2df,p) basis sets) levels. The calculated frequencies and the Raman and infrared (IR) intensities were compared with the experimental results. Excellent agreement between calculated and observed vibrational wavenumbers was obtained. Additionally, a normal coordinate analysis (NCA) was also done by using the normal mode eigenvectors obtained at the B3LYP/6–311++G(3df,3pd) level. All fundamental vibrational bands were assigned to the normal modes with the aid of the potential energy distribution (PED) values obtained from normal coordinate calculations. To study the internal rotation of CH3groups, single CH3rotation and synchronous rotations of both CH3groups (clockwise–clockwise and clockwise–counterclockwise) were analyzed using the MP2/6–311++G(3df,2pd) and B3LYP/6–311++G(3df,2pd) levels.

scholarly journals Thermal desorption of formamide and methylamine from graphite and amorphous water ice surfaces

2018 ◽  
Vol 612 ◽  
pp. A47 ◽  
Author(s):  
H. Chaabouni ◽  
S. Diana ◽  
T. Nguyen ◽  
F. Dulieu
Keyword(s):  
Energy Distribution ◽  
Gas Phase ◽  
Thermal Desorption ◽  
Binding Energies ◽  
Desorption Energy ◽  
Exponential Factor ◽  
Water Ice ◽  
Ice Surface ◽  
Ice Surfaces ◽  
Best Fit

Context. Formamide (NH2CHO) and methylamine (CH3NH2) are known to be the most abundant amine-containing molecules in many astrophysical environments. The presence of these molecules in the gas phase may result from thermal desorption of interstellar ices. Aims. The aim of this work is to determine the values of the desorption energies of formamide and methylamine from analogues of interstellar dust grain surfaces and to understand their interaction with water ice. Methods. Temperature programmed desorption (TPD) experiments of formamide and methylamine ices were performed in the sub-monolayer and monolayer regimes on graphite (HOPG) and non-porous amorphous solid water (np-ASW) ice surfaces at temperatures 40–240 K. The desorption energy distributions of these two molecules were calculated from TPD measurements using a set of independent Polanyi–Wigner equations. Results. The maximum of the desorption of formamide from both graphite and ASW ice surfaces occurs at 176 K after the desorption of H2O molecules, whereas the desorption profile of methylamine depends strongly on the substrate. Solid methylamine starts to desorb below 100 K from the graphite surface. Its desorption from the water ice surface occurs after 120 K and stops during the water ice sublimation around 150 K. It continues to desorb from the graphite surface at temperatures higher than160 K. Conclusions. More than 95% of solid NH2CHO diffuses through the np-ASW ice surface towards the graphitic substrate and is released into the gas phase with a desorption energy distribution Edes = 7460–9380 K, which is measured with the best-fit pre-exponential factor A = 1018 s−1. However, the desorption energy distribution of methylamine from the np-ASW ice surface (Edes = 3850–8420 K) is measured with the best-fit pre-exponential factor A = 1012 s−1. A fraction of solid methylamine monolayer of roughly 0.15 diffuses through the water ice surface towards the HOPG substrate. This small amount of methylamine desorbs later with higher binding energies (5050–8420 K) that exceed that of the crystalline water ice (Edes = 4930 K), which is calculated with the same pre-exponential factor A = 1012 s−1. The best wetting ability of methylamine compared to H2O molecules makes CH3NH2 molecules a refractory species for low coverage. Other binding energies of astrophysical relevant molecules are gathered and compared, but we could not link the chemical functional groups (amino, methyl, hydroxyl, and carbonyl) with the binding energy properties. Implications of these high binding energies are discussed.

scholarly journals Computing Binding Energies of Interstellar Molecules by Semiempirical Quantum Methods: Comparison Between DFT and GFN2 on Crystalline Ice

2021 ◽  
pp. 632-645
Author(s):  
Aurèle Germain ◽  
Marta Corno ◽  
Piero Ugliengo
Keyword(s):  
Gas Phase ◽  
Water Clusters ◽  
Binding Energies ◽  
Water Ice ◽  
Small Water ◽  
Adsorption Processes ◽  
Quantum Approach ◽  
Crystalline Water ◽  
Ordered Water ◽  
Grain Surface

AbstractInterstellar Grains (IGs) spread in the Interstellar Medium (ISM) host a multitude of chemical reactions that could lead to the production of interstellar Complex Organic Molecules (iCOMs), relevant in the context of prebiotic chemistry. These IGs are composed of a silicate-based core covered by several layers of amorphous water ice, known as a grain mantle. Molecules from the ISM gas-phase can be adsorbed at the grain surfaces, diffuse and react to give iCOMs and ultimately desorbed back to the gas phase. Thus, the study of the Binding Energy (BE) of these molecules at the water ice grain surface is important to understand the molecular composition of the ISM and its evolution in time. In this paper, we propose to use a recently developed semiempirical quantum approach, named GFN-xTB, and more precisely the GFN2 method, to compute the BE of several molecular species at the crystalline water ice slab model. This method is very cheap in term of computing power and time and was already showed in a previous work to be very accurate with small water clusters. To support our proposition, we decided to use, as a benchmark, the recent work published by some of us in which a crystalline model of proton-ordered water ice (P-ice) was adopted to predict the BEs of 21 molecules relevant in the ISM. The relatively good results obtained confirm GFN2 as the method of choice to model adsorption processes occurring at the icy grains in the ISM. The only notable exception was for the CO molecule, in which both structure and BE are badly predicted by GFN2, a real pity due to the relevance of CO in astrochemistry.

Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

2019 ◽  
Author(s):  
Drew P. Harding ◽  
Laura J. Kingsley ◽  
Glen Spraggon ◽  
Steven Wheeler
Keyword(s):  
Gas Phase ◽  
Electrostatic Interactions ◽  
Density Functional ◽  
Molecular Descriptors ◽  
Stacking Interactions ◽  
Interaction Energies ◽  
Functional Theory ◽  
Binding Partner ◽  
Heavy Atoms ◽  
Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

Investigation of Adsorption Effect of Carbon Monoxide on Coniine: A DFT Study

2021 ◽  
Vol 17 ◽  
Author(s):  
Siyamak Shahab ◽  
Masoome Sheikhi ◽  
Mehrnoosh Khaleghian ◽  
Marina Murashko ◽  
Mahin Ahmadianarog ◽  
...  
Keyword(s):  
Carbon Monoxide ◽  
Gas Phase ◽  
Density Functional ◽  
Energy Gap ◽  
Adsorption Effect ◽  
Chemical Shift Tensors ◽  
Solvent Water ◽  
Donor And Acceptor ◽  
Before And After ◽  
Electron Donor And Acceptor

: For the first time in the present study, the non-bonded interaction of the Coniine (C8H17N) with carbon monoxide (CO) was investigated by density functional theory (DFT/M062X/6-311+G*) in the gas phase and solvent water. The adsorption of the CO over C8H17N was affected on the electronic properties such as EHOMO, ELUMO, the energy gap between LUMO and HOMO, global hardness. Furthermore, chemical shift tensors and natural charge of the C8H17N and complex C8H17N/CO were determined and discussed. According to the natural bond orbital (NBO) results, the molecule C8H17N and CO play as both electron donor and acceptor at the complex C8H17N/CO in the gas phase and solvent water. On the other hand, the charge transfer is occurred between the bonding, antibonding or nonbonding orbitals in two molecules C8H17N and CO. We have also investigated the charge distribution for the complex C8H17N/CO by molecular electrostatic potential (MEP) calculations using the M062X/6-311+G* level of theory. The electronic spectra of the C8H17N and complex C8H17N/CO were calculated by time dependent DFT (TD-DFT) for investigation of the maximum wavelength value of the C8H17N before and after the non-bonded interaction with the CO in the gas phase and solvent water. Therefore, C8H17N can be used as strong absorbers for air purification and reduce environmental pollution.

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