ONIOM(QM:AMOEBA09) Study on Binding Energies and Binding

Subscriber access provided by NEW YORK UNIV

Article

ONIOM(QM:AMOEBA09) Study on Binding Energies and Binding Preference of OH, HCO, and CH Radicals on Hexagonal Water Ice (I) 3

h

W. M. Chamil Sameera, Bethmini Senevirathne, Stefan Andersson, Feliu Maseras, and Gunnar Nyman J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.7b04105 • Publication Date (Web): 20 Jun 2017 Downloaded from http://pubs.acs.org on July 4, 2017

Just Accepted “Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted online prior to technical editing, formatting for publication and author proofing. The American Chemical Society provides “Just Accepted” as a free service to the research community to expedite the dissemination of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully peer reviewed, but should not be considered the official version of record. They are accessible to all readers and citable by the Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore, the “Just Accepted” Web site may not include all articles that will be published in the journal. After a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web site and published as an ASAP article. Note that technical editing may introduce minor changes to the manuscript text and/or graphics which could affect content, and all legal disclaimers and ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or consequences arising from the use of information contained in these “Just Accepted” manuscripts.

The Journal of Physical Chemistry C is published by the American Chemical Society. 1155 Sixteenth Street N.W., Washington, DC 20036 Published by American Chemical Society. Copyright © American Chemical Society. However, no copyright claim is made to original U.S. Government works, or works produced by employees of any Commonwealth realm Crown government in the course of their duties.

Page 1 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

The Journal of Physical Chemistry

ONIOM(QM:AMOEBA09) Study on Binding Energies and Binding Preference of OH, HCO, and CH3 Radicals on Hexagonal Water Ice (Ih) W. M. C. Sameera,1,2* Bethmini Senevirathne,1 Stefan Andersson,1,3 Feliu Maseras4,5 and Gunnar Nyman1 1

University of Gothenburg, Department of Chemistry and Molecular Biology, Kemigården 4,

SE-412 96 Gothenburg, Sweden. 2

Department of Chemistry, Faculty of Science, Hokkaido University, Kita-Ku, Sapporo, 060-

0810, Japan. 3

SINTEF Materials and Chemistry, P.O. Box 4760, NO-7465 Trondheim, Norway.

4

Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007

Tarragona, Catalonia, Spain. 5

Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia,

Spain.

ABSTRACT. We have combined the AMOEBA09 polarizable force field with the ONIOM(QM:MM) method to rationalize binding energies and binding preferences of the OH, HCO, and CH3 radicals on crystalline water ice (Ih). ONIOM(M062X:AMOEBA09) and ONIOM(wB97XD:AMOEBA) calculations suggest that the dangling hydrogen (d-H) or dangling oxygen (d-O) on the binding sites play an important role on the binding energies.

ACS Paragon Plus Environment

1


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 2 of 26

Depending on the dangling nature at the binding site, a range of binding energies is found for the OH radical (0.67 – 0.20 eV), HCO radical (0.42 – 0.12 eV), and CH3 radical (0.26 – 0.11 eV). The binding energies of these radicals are larger in the presence of both d-H and d-O at the binding site. On the other hand, binding energies are weaker in the presence of only d-H or d-O at the binding site. The ONIOM(QM:AMOEBA09) methodology is found to be a useful approach to calculate binding energies of atoms, radicals, and molecules on Ih.

Introduction The interstellar medium (ISM) contains a range of atoms, radicals, and molecules including several organic species. Almost 200 molecules have been identified in the ISM or circumstellar shells from their rotational, vibrational, or electronic spectra.1 Despite numerous experimental and computational studies, the origin of the molecular species in the ISM and the mechanistic details of their formation and reactions are still not fully understood. Radical species in the ISM play an important role in the formation of more complex molecules. Many chemical processes occur on icy mantles of interstellar grains. Relatively simple radicals, the so-called primary radicals (H, OH, CO, HCO, CH3O, CH2OH, CH3, NH, and NH2) in the ISM may be formed at icy mantles through cosmic ray-induced photodissociation of the ice mantle constituents, such as H2O, CH4, H2CO, CH3O, NH3, or through surface reactions between atoms, radicals and molecules such as CO and O2.2,3 The primary radical species adsorb to icy mantles, diffuse on the surface, and react with each other to form more complex molecules or radicals. The radicals may also desorb and react further in the gas phase. The adsorption strengths of the radicals will determine their desorption probability and influence their surface mobility, both of which are critical in determining their reactivity. These chemical processes are often complex and difficult to


2

Page 3 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


characterize unambiguously from experimental studies, whereby computational studies become critical. In the present study, we apply the ONIOM(QM:AMOEBA09) method to rationalize binding energies and binding preference of three primary radical species, specifically OH, HCO, and CH3 on hexagonal ice (Ih). Over the past years, several computational studies have been reported for complexes of H2O with a radical (H2O-H,4-7 H2O-OH,8-16 H2O-HCO,17-18 H2O-CH3,19 H2O-NO,20 H2O-NO2,21 H2O-HO2,22 H2O-ClO,23 H2O-OClO and H2O-ClOO24,25). These simple complexes can be used as model systems to understand radical binding on ices. Small radicals often interact with the H2O molecule through a single-electron hydrogen bond (either as an H-bond acceptor or as an H-bond donor). In the ISM, the OH radical can be formed through photodissociation of H2O or through surface reactions between O and H atoms. For the simple H2O-OH complex, three low-energy minima are possible (Scheme 1).11,12,26 In the global minimum (Scheme 1a), hydrogen bonding occurs between the hydrogen atom of the OH radical and the oxygen atom of the water molecule. Apart from this, two closely lying local minimum structures were also located (Scheme 1b and Scheme 1c), where hydrogen bonding occurs between the oxygen atom of the hydroxyl radical and a hydrogen atom of the water molecule.12,26 Removing the hydroxyl radical from the H2O-OH complex requires 0.24 eV at the CCSD(T)/CBS level of theory.11 A similar binding energy was suggested by Garrod and Herbst.27 Several studies have been performed for OH-(H2O)n cluster models,14,28-33 and these systems can be considered as more realistic models to replicate ice surfaces.

Scheme 1. Reported low-energy minima for the H2O-OH complex.11,12,26


3


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 4 of 26

The HCO radical is a key species for the synthesis of carboxylic acids, aldehydes, and alcohols in cold interstellar clouds.34-36 According to Pirim et al.37 and van Ijzendoorn et al.38 the HCO radical can be formed from H and CO (at 3-10 K) through an effectively very low reaction barrier. On the basis of quantum rate calculations, Andersson et al.39 argued that highly efficient quantum tunneling accounts for the low effective barrier, since considering only the classical over-the-barrier reaction would predict practically zero reaction probability at the low temperatures considered.39 Based on CCSD(T)/aug-cc-pVTZ calculations, three structures were proposed for the HCO-H2O complex.17 The most stable form is a cyclic structure, which contains C−H···O and O−H···O  hydrogen bonds. Two relatively unstable linear structures are also possible. In one of them, a hydrogen atom of water interacts with  the oxygen atom of the HCO radical. In the other linear structure, the hydrogen atom of the HCO radical interacts with  the oxygen atom of water. Another important radical species in the ISM is the CH3 radical, which can be formed through the addition of H atoms to a carbon atom or the reaction of methane with an OH radical.40 In the CH3-H2O complex, the methyl radical (CH3) often behaves as a proton acceptor. Ab initio calculations of its optimized geometry predict a weakly bonded complex of Cs symmetry. In this structure, one of the H atoms of the water molecule points towards the carbon atom of the methyl radical.41,42 Ices in the ISM are mainly amorphous, but may also exist in crystalline phases. Interactions between radicals and ice surfaces are complex, and the simple H2O-radical complexes may be insufficient to describe the behavior of the radicals on crystalline (or amorphous) ices. Hexagonal ice, the common form of crystalline ice under ambient conditions, can be used as a host to study various chemical processes. Compared to simple radical-H2O complexes, hexagonal ice is a more realistic model to replicate icy mantles of interstellar grains. At a hexagonal unit, the three water molecules in the bottom obey the “ice rules”. However, water molecules in the top are three-coordinated, and do not follow the ice rule. Therefore, these


4

Page 5 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


water molecules contribute either a dangling-hydrogen (d-H) or dangling-oxygen (d-O) to the surface.43,44 The pattern of the dangling atoms on the ice surface therefore plays an important role in the interaction between the ice surface and the adsorbent.45 In terms of computational methods, molecular dynamics (MD) simulations can be used to study chemical processes on interstellar grains, often with periodic boundary conditions. However, it is important to note that the empirical parameters of the commonly used force fields or user-defined force fields are often determined from a limited number of model systems. Therefore, the accuracy of MD simulations depends on the quality of the original parameterization and transferability of the parameters to new molecular environments. This is however less dramatic in the case of density functional theory (DFT) than the force field approach. Therefore, DFT-based MD methods, Car-Parrinello Molecular Dynamics (CPMD) for instance, may be more accurate, but significantly more demanding. Small cluster models of ices can be modeled with DFT or ab initio methods. In the case of DFT, it is important to note that the calculated properties may depend on the chosen density functional. Structure deformation is a common problem in the cluster model approach, which ultimately leads to unrealistic ice structures. These issues inspired us to use a hybrid quantum mechanics/molecular mechanics (QM/MM) method for binding energies and binding preference of OH, HCO, and CH3 radicals on Ih.

Computational methods In this study, we have used the Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM)46-50 method to calculate binding energies of OH, HCO, and CH3 radical species on Ih. In a two-layer ONIOM approach, the electronically important part can be


5


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 6 of 26

described by quantum mechanics (QM), while the remaining part can be described by molecular mechanics (MM), the so-called ONIOM(QM:MM). The ONIOM(QM:MM) method has been applied to a range of problems in chemical, biological, and material sciences.51-53 However, applications of ONIOM(QM:MM) to astrochemical systems, crystalline or amorphous ices for instance, are not easy due to the fact that the commonly used ONIOM(QM:MM) implementations do not have suitable force fields for modeling water ice. It is important to note that the commonly used ONIOM(QM:UFF) (UFF – universal force field) in the Gaussian0954 program cannot be used for this purpose due to the fact that the UFF description in the MM region causes structural deformations (Figure 1). This problem can be avoided by using an ONIOM(QM:AMOEBA09) method, where the AMOEBA09 polarizable force field does not lead to such structural deformations. The AMOEBA0955-57 force field includes permanent electrostatic multipole moments through the quadrupole at each atom as well as distributed atomic polarizabilities. This provides a more accurate description for electrostatic potentials, hydrogen bonding, and other interactions. Therefore, an ONIOM(QM:AMOEBA09) method should be appropriate for modeling chemical processes on ices. In this work, the ONIOM(QM:AMOEBA09) calculations were performed with an in-house program, which we intend to make freely accessible in the near future.


6

Page 7 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Top view

Top view

Side view

Side view

(a)

(b)

Figure 1. (a) ONIOM(M062X:AMOEBA09) ice model structure after 100 optimization cycles. (b) ONIOM(M062X:UFF) ice model structure after 100 optimization cycles. Structure optimizations were started from the same initial model structure. The QM region, consisting of 12 H2O molecules, is in “ball and sticks” and the MM region, consisting of 150 H2O molecules, is in “wireframe”. In this study, we have used eight crystalline ice cluster models to replicate the possible binding sites on hexagonal ice (vide infra), and optimized them with the ONIOM(QM:AMOEBA09) method. For the AMOEBA09 calculations, we have used the AMOEBA09 atom type definitions “water O” for oxygen, “water H” for hydrogen, and “alkane –CH3” for carbon. In the QM/MM model structures of Ih, the QM and MM regions are not covalently linked, and therefore the problem of the QM/MM boundary is rather simple. The mechanical embedding (ME) scheme was used here for this purpose, where the interactions between the QM and MM regions were calculated by the AMOEBA09 force


7


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 8 of 26

field. In our study, QM/MM cluster model structures of the binding sites were fully optimized with two methods; ONIOM(M062X:AMOEBA09) and ONIOM(wB97XD:AMOEBA09). The M062X and wB97XD density functionals have been shown to perform well for binding energies of water clusters and surfaces. 58-59 Therefore, we have used these two density functionals for the QM part. The 6-31+G(d,p) basis sets were used for the atoms in the QM region.60-63 The counterpoise approach was used to determine the basis set superposition error (BSSE).64-65

Figure 2. Top and side views of the QM/MM ice cluster models A and B (QM region is in “ball and sticks” and MM region in “wireframe”), and dangling features (d-H and d-O) on the top layer of the eight binding sites. Black circles show d-H, orange circles show d-O, while blue circles show the O atoms in the layer immediately below.

Ice models and binding sites Ice cluster models were built by using the crystalline water ice (Ih) structural models of Cuppen and co-workers.66 We have used two types of models to replicate possible binding sites (Figure 2). Three water layers were included in both types of models. The first model, A, is composed of 162 H2O molecules, while the second model (B) has 156 H2O molecules.


8

Page 9 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


In A, the QM region is composed of 24 H2O molecules, and the remaining 138 H2O molecules are included in the MM region. In the case of B, 20 H2O molecules are in the QM region, and the remaining 136 H2O molecules are included in the MM region. In both models A and B, we have used relatively large MM regions to avoid structural deformations of the binding pocket upon structure optimization. The outermost H2O molecules were frozen to save computational cost. Depending on the number of d-H and d-O atoms in the top layer of the QM region, eight different binding sites, four from A (A1, A2, A3, A4) and four from B (B1, B2, B3, B4), are possible (Figure 2). A1 and B1 consist of two d-Hs and one d-O, while A2 and B2 hold one d-H and two d-Os. The A3 and B3 binding sites consist of three d-Os, and A4 and B4 consist of three d-Hs. In the present paper, we focus only on crystalline water ice (Ih) structural models, which have eight binding sites. In amorphous water ice, additional types of binding sites can be found due to complex reorganizations of water molecules on the surface. In previous studies on CO67 and H68 atom binding to ice surfaces, broader ranges of binding energies were found on amorphous than on crystalline surfaces. This could possibly be the case for OH, HCO, and CH3, but explicit calculation thereof is beyond the scope of the present paper.

Results and discussions OH radical binding on crystalline water ice (Ih) Fully optimized ice structures with an OH radical are shown in Figure 3, and their binding energies are summarized in Table 1. The M062X optimized structure of an isolated OH radical has an O-H bond distance of 0.98 Å. ONIOM(M062X:AMOEBA09) calculations suggested that the adsorbed OH radical at the eight binding sites preserves its structure (i.e. the O-H bond distance is 0.98 – 0.99 Å). The A1 site has an OH binding energy of 0.57 eV,


9


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 10 of 26

while the binding energy of B1 is marginally larger (0.61 eV). At A1 and B1, the hydrogen atom of the OH radical interacts with a d-O of the surface, and the oxygen of the OH radical interacts with two surface d-Hs, leading to three hydrogen bonds. In the case of A2 (0.67 eV) and B2 (0.55 eV) binding sites, one d-H and two d-Os are present. This dangling nature supports OH radical binding through two hydrogen bonds. In the presence of two or three hydrogen bonds, the OH radical adsorbs strongly at the A1, A2, B1, and B2 binding sites. A3 and B3 binding sites have only d-Os, and therefore the OH radical can form a single hydrogen bond between its H atom and a surface d-O. As a result, binding energies are weaker at A3 (0.37 eV) and B3 (0.43 eV). At the remaining two binding sites (i.e. A4 and B4), relatively weak hydrogen bonds are formed between one of the oxygen atom lone-pairs of the OH radical and two surface d-Hs, leading to relatively weak binding energies (0.20 eV at A4 and 0.28 eV at B4).

1.96

2.28 1.84

111.7 120.6 2.45

114.0

2.48 114.8 2.18 100.6

2.08 114.5

0.37 A3 1.81

0.55 B2

0.20 A4

2.32

1.85 90.3

0.61 B1

2.30 105.6

1.83

0.67 A2

0.57 A1 1.89

2.42 1.80

117.5 2.56

0.43 B3

0.28 B4

Figure 3. ONIOM(M062X:AMOEBA09) optimized structures of the OH radical binding sites, and their binding energies (eV). Only the binding pocket of the QM region is shown for simplicity. Bond lengths (blue) are in Å and bond angles (green) are in degrees. In summary, ONIOM(M062X:AMOEBA09) calculations suggest that the d-H and d-O features on Ih play an important role on the binding energies of the OH radical, where a range


10

Page 11 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


of binding energies were found. The binding preference follows the order A2 (0.67 eV) > B1 (0.61 eV) > A1 (0.57 eV) > B2 (0.55 eV) > B3 (0.43 eV) > A3 (0.37 eV) > B4 (0.28 eV) > A4 (0.20 eV). The calculated average OH radical binding energy of 0.43 eV is in agreement with the value of 0.40 eV from temperature programmed desorption (Dulieu et al.69) and the computed value of 0.40 eV (Wakelam et al.70). In the latter case, they assumed that the binding energy of the radical with amorphous solid water is proportional to the interaction energy between a water molecule and the radical. The proportionality coefficients were calculated by fitting the experimental binding energies and the calculated intermolecular energy of a water molecule dimer. Table 1. Binding energies (without ZPE corrections) of the OH, HCO, and CH3 radicals from ONIOM(MO62X:AMOEBA09) and ONIOM(wB97XD:AMOEBA09) optimized structures. Values in parenthesis are from DFT single-point energies for the full system (values in italic are the calculated binding energies accounting for BSSE). Binding energy (eV) from ONIOM(M062X:AMOEBA09) Radical A1

A2

A3

A4

B1

B2

B3

B4

OH

0.57 [0.53] [0.58]

0.67 [0.61] [0.66]

0.37 [0.37] [0.42]

0.20 [0.20] [0.25]

0.61 [0.57] [0.62]

0.55 [0.52] [0.58]

0.43 [0.52] [0.59]

0.28 [0.26] [0.32]

HCO

0.36 [0.30] [0.33]

0.42 [0.36] [0.39]

0.34 [0.30] [0.34]

0.17 [0.20] [0.24]

0.39 [0.31] [0.36]

0.36 [0.32] [0.35]

0.22 [0.29] [0.32]

0.12 [0.13] [0.17]

CH3

0.26 [0.23] [0.26]

0.24 [0.22] [0.25]

0.11 [0.09] [0.13]

0.14 [0.15] [0.19]

0.27 [0.27] [0.30]

0.23 [0.20] [0.24]

0.21 [0.23] [0.27]

0.19 [0.12] [0.15]

Binding energy (eV) from ONIOM(wB97XD:AMOEBA09) Radical A1

A2

A3

A4

B1

B2

B3

B4

OH

0.47 [0.47]

0.66 [0.61]

0.41 [0.38]

0.15 [0.15]

0.58 [0.52]

0.51 [0.52]

0.39 [0.39]

0.30 [0.33]

HCO

0.31

0.43

0.26

0.13

0.40

0.33

0.18

0.03


11


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

CH3

Page 12 of 26

[0.28]

[0.34]

[0.28]

[0.17]

[0.37]

[0.31]

[0.26]

[0.06]

0.13 [0.14]

0.21 [0.20]

0.06 [0.02]

0.13 [0.15]

0.28 [0.30]

0.18 [0.17]

0.13 [0.18]

0.13 [0.10]

In order to check the effects of the chosen density functional, we have calculated the binding energies with ONIOM(wB97XD:AMOEBA09), where the optimized structures and binding energies show minor deviations from the ONIOM(M062X:AMOEBA09) results (Table 1, Figure 4a). In order to check the effect of the size of the QM region on calculated binding energies, we have compared the binding energies from ONIOM(M062X:AMOEBA09) and M062X single-point energies for the full system (Table 1, Figure 4a), and found good agreement. Further, the maximum absolute discrepancy between ONIOM(MO62X:AMOEBA09) and M062X is 0.09 eV for the OH radical, 0.08 eV for the HCO radical, and 0.07 eV for the CH3 radical. The maximum relative discrepancy is around 20% for the OH and HCO radicals, and 40% eV for the CH3 radical. The corresponding values for ONIOM(wB97XD:AMOEBA09) and wB97XD are 0.06 eV (9%) for OH, 0.09 eV (20%) for HCO, and 0.05 eV (40%) for CH3 (Table 1, Figure 4b). Therefore, we argue that the size of the QM region in our ONIOM(QM:MM) model systems is large enough to provide accurate binding energies. Similar conclusions can be made from calculated dipole moments (Table S1, Supporting Information). The role of the BSSE was evaluated for the M062X binding energies (Table1). We have found that the BSSE plays a minor role, where the maximum absolute deviations of the binding energies are 0.06 eV for the OH radical, 0.05eV for the HCO radical, and 0.04 eV for the CH3 radical. We have extended the modeling aspects discussed above to study the binding energies and binding preference of the CH3 and HCO radicals on Ih, which is the subject of the next subsection.


12

Page 13 of 26

ONIOM(M062X:AMOEBA09)

M062X

ONIOM(wB97XD:AMOEBA09)

0.7

0.7

0.6

0.6

0.5

0.5

Binding energy (eV)

Binding energy (eV)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


0.4 0.3 0.2 0.1

wB97XD

0.4 0.3 0.2 0.1

0.0

0.0

A1

A2

A3

A4

B1

B2

B3

B4

A1

A2

(a)

A3

A4

B1

B2

B3

B4

(b)

Figure 4. Calculated binding energies (eV) of OH radicals on crystalline hexagonal water ice (Ih) from; (a) ONIOM(M062X:AMOEBA09) and M062X, (b) ONIOM(M062X:wB97XD) and wB97XD.

HCO and CH3 radical binding on crystalline water ice (Ih) ONIOM(M062X:AMOEBA09) optimized structures of the HCO radical bound at the ice structures are shown in Figure 5a. The M062X optimized structure of an isolated HCO radical has a bent structure [r(H-C) = 1.12 Å, r(C-O) = 1.18 Å, and A(H-C-O) = 123.80]. Upon adsorption to the ice surface, the HCO radical nearly preserves its structure [r(H-C) = 1.11 - 1.13 Å, r(C-O) = 1.17 - 1.19 Å, and A(H-C-O) = 124.2 – 125.90]. Compared to the OH radical binding energies, the HCO radical binding energies are weaker at all binding sites (Table 1, Figure 5a, Figure 6a, 6b). The HCO radical binding energy is relatively strong at A1 (0.36 eV), B1 (0.39 eV), A2 (0.42 eV) and B2 (0.36 eV), where interactions between the H atom or O atom of the HCO radical and the surface d-Os or d-Hs establish two or three hydrogen bonds. Moving to A3 (0.34 eV) and B3 (0.22 eV), the binding energies become weaker due to the fact that only one hydrogen bond, between the hydrogen atom of HCO and


13


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 14 of 26

a surface d-O, can be formed. At A4 (0.17 eV) and B4 (0.12 eV), only one hydrogen bond, between the oxygen atom of HCO and a surface d-H, is formed, and therefore the binding energy is weaker.

(a)

(b) Figure 5. ONIOM(M062X:AMOEBA09) optimized structures of (a) the HCO radical and (b) the CH3 radical binding sites, and their binding energies (eV). Only the binding pocket of the QM region is shown for simplicity. Bond lengths (blue) are in Å and bond angles (green) are in degrees.


14

Page 15 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Based on the ONIOM(M062X:AMOEBA09) binding energies, the HCO radical binding preference follows the order A2 > B1 > A1 = B2 > A3 > B3 > A4 > B4. The calculated average HCO radical binding energy on crystalline water ice (Ih) from ONIOM(M062X:AMOEBA09) and ONIOM(wB97XD:AMOEBA09) are 0.30 eV and 0.26 eV, respectively. Relatively small binding energies were reported in the literature (partly due to fewer H2O molecules in the model calculations); there is an estimated value of 0.14 eV by Garrod and Herbst,27 and calculated values of 0.21 eV (Wakelam et al.)70 and 0.20 eV (Enrique-Romero et al.)71. ONIOM(M062X:AMOEBA09) optimized structures of the CH3 radical complexes are shown in Figure 5b. The CH3 radical binding energies on crystalline water ice (Ih) is substantially weaker than the OH radical or HCO radical binding energies (Table 1, Figure 6c, 6d). The CH3 radical also preserves its structure upon adsorption at the surface [M062X optimized structures of an isolated CH3 radical: r(O-H) = 1.08 Å and A(H-C-H) = 119.90]. The CH3 radical binding energies are 0.26 eV at the A1 site, 0.24 eV at A2, 0.27 eV at B1 and 0.23 eV at B2. Relatively weak binding energies can be seen at the remaining four binding sites [A3 (0.11 eV), A4 (0.14 eV), B3 (0.21 eV), and B4 (0.19 eV)]. Based on the ONIOM(M062X:AMOEBA09) binding energies, the CH3 radical binding preference follows the order B1 > A1 > A2 > B2 > B3 > B4 > A4 > A3. The average CH3 radical binding energy from ONIOM(M062X:AMOEBA09) is 0.20 eV, while the ONIOM(wB97XD:AMOEBA09) average binding energy is 0.16 eV. Therefore, the CH3 radical adsorption at crystalline hexagonal water ice (Ih), even though comparably weak, can occur. Our calculated average binding energy, 0.20 eV with the ONIOM(M062X:AMOEBA09) method and 0.16 eV with the ONIOM(wB97XD:AMOEBA09) method, is larger than the calculated values (0.14 eV of Wakelam et al.70 and 0.06 eV of Enrique-Romero et al.71), perhaps due to the fact that the CH3 radical in pure model systems interact with more than one H2O molecule on the surface.


15


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 16 of 26

(a)

(b)

(c)

(d)

Figure 6. Calculated binding energies (eV) of HCO radicals on crystalline hexagonal water ice (Ih) from; (a) ONIOM(M062X:AMOEBA09) and M062X, (b) ONIOM(M062X:wB97XD) and wB97XD. Calculated binding energies (eV) of CH3 radicals on crystalline hexagonal water ice (Ih) from; (c) ONIOM(M062X:AMOEBA09) and M062X, (d) ONIOM(M062X:wB97XD) and wB97XD.


16

Page 17 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Our calculations suggest that the binding energies of OH, HCO, and CH3 radicals on crystalline hexagonal water ice (Ih) are sensitive to the dangling nature (i.e. d-O and d-H) at the binding sites. As a result, a range of binding energies can be observed. OH, HCO, and CH3 radicals bind strongly at the A1, A2, B1, and B2 binding sites, where a mixture of d-O and d-H can be found. The remaining four binding sites (A3, A4, B3, and B4) have only three d-Os or three d-Hs, and show weaker radical binding energies.

Conclusions In this study, we have used an ONIOM(QM:AMOEBA09) method to calculate the binding energies of OH, HCO, and CH3 radicals on crystalline water ice (Ih). The ONIOM(QM:AMOEBA09) approach is computationally efficient, and therefore relatively large ice models can be studied. In this approach, a binding site can be modeled with a QM method, and therefore binding energies can be calculated to well-controlled accuracy. Depending on the dangling nature of the binding site, a range of binding energies are obtained for the OH, HCO, and CH3 radicals on Ih [from ONIOM(M062X:AMOEBA09): OH radical binding energies: 0.67 – 0.20 eV, HCO radical: 0.42 – 0.12 eV, CH3 radical: 0.26 – 0.11 eV]. Calculated ONIOM(M062X:AMOEBA09) average binding energies of the three radicals follow the order of OH (0.46 eV) > HCO (0.30 eV) > CH3 (0.20 eV). The same trend was obtained from the ONIOM(wB97XD:AMOEBA09) method; OH (0.43 eV) > HCO (0.26 eV) > CH3 (0.16 eV). Diffusion rates are likely to follow the opposite order: OH < HCO < CH3. Calculated binding energies of the three radicals are relatively larger at the A1, A2, B1 and B2 sites that hold both d-Os and d-Hs. The radical binding energies on the A3, A4, B3, and B4 sites are relatively weaker, where there are only d-Os (A3, B3) or only d-Hs (A4, B4). Therefore, the distribution of d-Os and d-Hs on ice surfaces plays a key role not only on the radical binding energies, but also on their diffusion rates. Such information is


17


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 18 of 26

very useful in developing the next generation of gas-grain chemical models for astrochemistry. The ONIOM(QM:AMOEBA09) methodology can be used for modeling chemical processes on ice surfaces, but also for modeling organic, organometallic, and biochemical systems in the future.

ASSOCIATED CONTENT Supporting Information. Table S1: calculated dipole moments, energies of the calculated structures, Cartesian coordinates of the optimized structures.

AUTHOR INFORMATION Corresponding Author *W. M. C. Sameera, E-mail: [email protected], Tel: +81-11-706-3819, Fax: +81-11-706-3447. Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

ACKNOWLEDGMENT We would like to acknowledge the MC-ITN (LASSIE) grant and the Gothenburg Centre for Advance Studies in Science and Technology for financial support, and C3SE for super computing facilities. Support from the Swedish Research Council is also acknowledged. REFERENCES


18

Page 19 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(1) http://www.astro.uni-koeln.de/cdms/molecules (2) Garrod, R. T.; Weaver, S. L. W.; Herbst, E., Complex chemistry in star forming regions: an expanded gas-grain warm-up chemical model. Astrophys J. 2008, 682 (1), 283-302. (3) Oberg, K. I. R.; van Dishoeck, E. F.; Linnartz, H.; Andersson, S., The effect of H2O on ice photochemistry. Astrophys J. 2010, 718 (2), 832-840. (4) Masuda, K.; Takahashi, J.; Mukai, T., Sticking probability and mobility of a hydrogen atom on icy mantle of dust grains. Astron Astrophys, 1998, 330 (2), 773-781. (5) Zhang, Q.; Sabelli, N.; Buch, V., Potential energy surface of H-H2O. J. Chem. Phys. 1991, 95 (2), 1080-1085. (6) Al-Halabi, A.; Kleyn, A. W.; van Dishoeck, E. F.; Kroes, G. J., Sticking of hydrogen atoms to crystalline ice surfaces: Dependence on incidence energy and surface temperature. J. Phys. Chem. B, 2002, 106 (25), 6515-6522. (7) Buch, V.; Zhang, Q., Sticking probability of H and D atoms on amorphous ice - a computational study. Astrophys J. 1991, 379 (2), 647-652. (8) Engdahl, A.; Karlstrom, G.; Nelander, B., The water-hydroxyl radical complex: A matrix isolation study. J. Chem. Phys. 2003, 118 (17), 7797-7802. (9) Langford, V. S.; McKinley, A. J.; Quickenden, T. I., Identification of H2O-HO in argon matrices. J. Am. Chem. Soc. 2000, 122 (51), 12859-12863. (10) Soloveichik, P.; O'Donnell, B. A.; Lester, M. I.; Francisco, J. S.; Mccoy, A. B., Infrared spectrum and stability of the H2O-HO Complex: Experiment and theory. J. Phys. Chem. A, 2010, 114 (3), 1529-1538. (11) Kim, K. S.; Kim, H. S.; Jang, J. H.; Kim, H. S.; Mhin, B. J.; Xie, Y. M.; Schaefer, H. F., Hydrogen-bonding between the water molecule and the hydroxyl radical (H2O-OH) - the 2a'' and 2a' minima. J. Chem. Phys. 1991, 94 (3), 2057-2062.


19


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 20 of 26

(12) Xie, Y. M.; Schaefer, H. F., Hydrogen-bonding between the water molecule and the hydroxyl Radical (H2O-OH) - the global minimum. J. Chem. Phys. 1993, 98 (11), 8829-8834. (13) Zhou, Z. Y.; Qu, Y. H.; Fu, A. P.; Du, B. N.; He, F. X.; Gao, H. W., Density functional complete study of hydrogen bonding between the water molecule and the hydroxyl radical (H2O-HO). Int. J. Quantum Chem. 2002, 89 (6), 550-558. (14) do Couto, P. C.; Guedes, R. C.; Cabral, B. J. C.; Simoes, J. A. M., The hydration of the OH radical: microsolvation modeling and statistical mechanics simulation. J. Chem. Phys. 2003, 119 (14), 7344-7355. (15) Codorniu-Hernandez, E.; Kusalik, P. G., Hydroxyl radicals in ice: insights into local structure and dynamics. Phys. Chem. Chem. Phys. 2012, 14 (33), 11639-11650. (16) Pabis, A.; Szala-Bilnik, J.; Swiatla-Wojcik, D., Molecular dynamics study of the hydration of the hydroxyl radical at body temperature. Phys. Chem. Chem. Phys. 2011, 13 (20), 9458-9468. (17) Cao, Q.; Berski, S.; Rasanen, M.; Latajka, Z.; Khriachtchev, L., Spectroscopic and computational characterization of the HCO-H2O Complex. J. Phys. Chem. A, 2013, 117 (21), 4385-4393. (18) Marenich, A. V.; Boggs, J. E., Coupled cluster CCSD(T) calculations of equilibrium geometries, anharmonic force fields, and thermodynamic properties of the formyl (HCO) and isoformyl (COH) radical species. J. Phys. Chem. A, 2003, 107 (13), 2343-2350. (19) Wang, B. Q.; Li, Z. R.; Wu, D.; Hao, X. Y.; Li, R. J.; Sun, C. C., Single-electron hydrogen bonds in the methyl radical complexes H3C-HF and H3C-HCCH: an ab initio study. Chem. Phys. Lett. 2003, 375 (1-2), 91-95. (20) Dozova, N.; Krim, L.; Alikhani, M. E.; Lacome, N., Vibrational spectra and structures of H2O-NO, HDO-NO, and D2O-NO complexes. An IR matrix isolation and DFT study. J. Phys. Chem. A, 2006, 110 (41), 11617-11626.


20

Page 21 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(21) Ball, D. W., DFT and G2 calculations on the NO2-H2O molecular complex. Chem. Phys. Lett. 1999, 312 (2-4), 306-310. (22) Nelander, B., The peroxy radical as hydrogen bond donor and hydrogen bond acceptor. A matrix isolation study. J. Phys. Chem. A, 1997, 101 (48), 9092-9096. (23) Francisco, J. S.; Sander, S. P., Existence of a chlorine oxide and water (Cl-H2O) radical complex. J. Am. Chem. Soc. 1995, 117 (39), 9917-9918. (24) Johnsson, K.; Engdahl, A.; Ouis, P.; Nelander, B., A matrix-isolation study of the water complexes of Cl2, ClOCl, OClO, and HOCl and their photochemistry. J. Phys. Chem. 1992, 96 (14), 5778-5783. (25) Aloisio, S.; Francisco, J. S., A density functional study of H2O-OClO, (H2O)2-OClO and H2O-ClOO complexes. Chem. Phys. 2000, 254 (1), 1-9. (26) Wang, B. S.; Hou, H.; Gu, Y. S., Density functional study of the hydrogen bonding: H2O-HO. Chem. Phys. Lett. 1999, 303 (1-2), 96-100. (27) Garrod, R. T.; Herbst, E., Formation of methyl formate and other organic species in the warm-up phase of hot molecular cores. Astron Astrophys, 2006, 457 (3), 927-936. (28) Du, S. Y.; Francisco, J. S.; Schenter, G. K.; Garrett, B. C., Many-body decomposition of the binding energies for OH-(H2O)2 and OH-(H2O)3 complexes. J. Chem. Phys. 2008, 128, 084307-8. (29) Belair, S. D.; Francisco, J. S.; Singer, S. J., Hydrogen bonding in cubic (H2O)8 and OH.(H2O)7 clusters. Phys. Rev. A, 2005, 71, 013204-10. (30) Tsuji, K.; Shibuya, K., Infrared spectroscopy and quantum chemical calculations of OH(H2O)n complexes. J. Phys. Chem. A, 2009, 113 (37), 9945-9951. (31) Du, S.; Francisco, J. S., Interaction between OH radical and the water interface. J. Phys. Chem. A, 2008, 112 (21), 4826-4835.


21


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 22 of 26

(32) Hamad, S.; Lago, S.; Mejias, J. A., A computational study of the hydration of the OH radical. J. Phys. Chem. A, 2002, 106 (39), 9104-9113. (33) Nanayakkara, A. A.; Balintkurti, G. G.; Williams, I. H., Barrier heights for hydrogen atom transfer reactions - evaluation of ab-initio molecular orbital methods for the degenerate exchange HO. + H2 -> H2O + .OH, J. Phys. Chem. 1992, 96 (9), 3662-3669. (34) Herbst, E., The chemistry of interstellar space. Chem. Soc. Rev. 2001, 30 (3), 168-176. (35) Woods, P. M.; Slater, B.; Raza, Z.; Viti, S.; Brown, W. A.; Burke, D. J., Glycolaldehyde formation via the dimerization of the formyl radical. Astrophys J, 2013, 777, 90, 7pp. (36) Rimola, A.; Taquet, V.; Ugliengo, P.; Balucani, N.; Ceccarelli, C., Combined quantum chemical and modeling study of CO hydrogenation on water ice. Astron. Astrophys. 2014, 572, A70, 12pp. (37) Pirim, C.; Krim, L., A neon-matrix isolation study of the reaction of non-energetic Hatoms with CO molecules at 3K. Phys. Chem. Chem. Phys. 2011, 13 (43), 19454-19459. (38) Vanljzendoorn, L. J.; Allamandola, L. J.; Baas, F.; Greenberg, J. M., Visible spectroscopy of matrix-isolated the 2A″(Π)←X 2A′ transition. J. Chem. Phys. 1983, 78 (12), 7019-7028. (39) Andersson, S.; Goumans, T. P. M.; Arnaldsson, A., Tunneling in hydrogen and deuterium atom addition to CO at low temperatures. Chem. Phys. Lett. 2011, 513 (1-3), 3136. (40) Zhang, B. L.; Zhang, J. H.; Liu, K. P., Imaging the "missing" bands in the resonanceenhanced multiphoton ionization detection of methyl radical. J. Chem. Phys. 2005, 122, 104310-4. (41) Hashimoto, T.; Iwata, S., Theoretical study on the weakly-bound complexes in the reactions of hydroxyl radical with saturated hydrocarbons (methane, ethane, and propane). J. Phys. Chem. A, 2002, 106 (11), 2652-2658.


22

Page 23 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(42) Rudic, S.; Merritt, J. M.; Miller, R. E., Study of the CH3-H2O radical complex stabilized in helium nanodroplets. Phys. Chem. Chem. Phys. 2009, 11 (26), 5345-5352. (43) Fletcher, N. H., Reconstruction of ice crystal surfaces at low temperatures, Philos. Mag. 1992, 66, 109-115. (44) Buch, V.; Groenzin, H.; Lit, I.; Shultz, M. J.; Tosatti, E., Proton order in the ice crystal surface. P. Natl. Acad. Sci. USA, 2008, 105 (16), 5969-5974. (45) Sun, Z. R.; Pan, D.; Xu, L. M.; Wang, E. G., Role of proton ordering in adsorption preference of polar molecule on ice surface. P. Natl. Acad. Sci. USA, 2012, 109 (33), 1317713181. (46) Maseras, F.; Morokuma, K., IMOMM - a new Integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states. J. Comput. Chem. 1995, 16 (9), 1170-1179; (47) Humbel, S.; Sieber, S.; Morokuma, K., The IMOMO method: Integration of different levels of molecular orbital approximations for geometry optimization of large systems: Test for n-butane conformation and SN2 reaction: RCl + Cl-. J. Chem. Phys. 1996, 105 (5), 19591967. (48) Svensson, M.; Humbel, S.; Morokuma, K., Energetics using the single point IMOMO (integrated molecular orbital plus molecular orbital) calculations: Choices of computational levels and model system. J. Chem. Phys. 1996, 105 (9), 3654-3661. (49) Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.; Sieber, S.; Morokuma, K., ONIOM: A multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition. J. Phys. Chem. 1996, 100 (50), 19357-19363.


23


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 24 of 26

(50) Matsubara, T.; Sieber, S.; Morokuma, K., A test of the new ''integrated MO+MM'' (IMOMM) method for the conformational energy of ethane and n-butane. Int. J. Quantum Chem. 1996, 60 (6), 1101-1109. (51) Sameera, W. M. C.; Maseras, F., Transition metal catalysis by density functional theory and density functional theory/molecular mechanics. Wires. Comput. Mol. Sci. 2012, 2 (3), 375-385; (52) Bo, C.; Maseras, F., QM/MM methods in inorganic chemistry. Dalton Trans, 2008, (22), 2911-2919. (53) Chung, L. W.; Sameera, W. M. C.; Ramozzi, R.; Page, A. J.; Hatanaka, M.; Petrova, G. P.; Harris, T. V.; Li, X.; Ke, Z.; Lui, F. et al., The ONIOM method and its applications, Chem. Rev. 2015, 115, 5678-5796. (54) Gaussian 09, Revision D.01, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A. et al., Gaussian, Inc., Wallingford CT, 2009. (55) Ponder, J. W.; Case, D. A., Force fields for protein simulations. Adv. Protein Chem. 2003, 66, 27-85; (56) Ren, P. Y.; Ponder, J. W., Polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B, 2003, 107 (24), 5933-5947. (57) Ren, P. Y.; Ponder, J. W., Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J. Comput. Chem. 2002, 23 (16), 1497-1506. (58) Sharma, D.; Sameera, W. M. C.; Andersson, S.; Nyman, G.; Paterson, M. J. Computational study of the interactions between benzene and crystalline ice Ih: Ground and excited states. ChemPhysChem, 2016, 177, 4079-4089.


24

Page 25 of 26

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


(59) Zhao, Y.; Schultz, N. E.; Truhlar, D. G., Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and non-covalent interactions. J. Chem. Theory. Comput. 2006, 2 (2), 364-382. (60) Ditchfie.R; Hehre, W. J.; Pople, J. A., Self-consistent molecular-orbital methods. Extended Gaussian-type basis for molecular-orbital studies of organic molecules. J. Chem. Phys. 1971, 54 (2), 724-728. (61) Hehre, W. J.; Ditchfie.R; Pople, J. A., Self-consistent molecular-orbital methods. Further extensions of Gaussian-type basis sets for use in molecular-orbital studies of organicmolecules. J. Chem. Phys. 1972, 56 (5), 2257-2261. (62) Harihara, P. C.; Pople, J. A., Influence of polarization functions on molecular-orbital hydrogenation energies. Theor. Chim. Acta, 1973, 28 (3), 213-222. (63) Francl, M. M.; Pietro, W. J.; Hehre, W. J.; Binkley, J. S.; Gordon, M. S.; Defrees, D. J.; Pople, J. A., Self-consistent molecular-orbital methods. A polarization-type basis set for 2nd row elements. J. Chem. Phys. 1982, 77 (7), 3654-3665. (64) Boys S. F.; Bernardi, F., Calculation of small molecular interactions by differences of separate total energies - some procedures with reduced errors,” Mol. Phys. 1970, 19, 553-556. (65) Simon, S.; Duran, M.; Dannenberg, J. J., How does basis set superposition error change the potential surfaces for hydrogen bonded dimers?, J. Chem. Phys., 1996, 105, 11024-31. (66) Karssemeijer, L. J.; Pedersen, A.; Jonsson, H.; Cuppen, H. M., Long-timescale simulations of diffusion in molecular solids. Phys. Chem. Chem. Phys. 2012, 14 (31), 1084410852. (67) Karssemeijer, L. J.; Ioppolo, S.; van Hemert, M. C.; van der Avoird, A.; Allodi, M. A.; Blake, G. A.; Cuppen, H. M., Dynamics of CO in amorphous water-ice environments, Astrophys J, 2014, 781, 16, 15pp.


25


1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

Page 26 of 26

(68) Senevirathne, B.; Andersson, S.; Dulieu, F.; Nyman, G.; Hydrogen atom mobility, kinetic isotope effects and tunneling on interstellar ices (Ih and ASW), Molecular Astrophysics, 2017, 6, 59-69. (69) Dulieu, F.; Congiu, E.; Noble, J.; Baouche, S.; Chaabouni, H.; Moudens, A.; Minissale, M.; Cazaux, S., How micron-sized dust particles determine the chemistry of our Universe. Sci. Rep. 2013, 3, 1338-1343. (70) Wakelama, V.; Mereaub, J.-C. L., R.; Ruauda, M.; Binding energies: new values and impact on the efficiency of chemical desorption. Molecular Astrophysics, 2017, 6, 22–35. (71) Enrique-Romero, J.; Rimola, A.; Ceccarelli, C.; Balucani, N., The (impossible?) formation of acetaldehyde on the grain surfaces: insights from quantum chemical calculations. Mon. Not. R. Astron. Soc. 2016, 459 (1), L6-L10.

TOC Graphic

Radical (OH, HCO, CH3) binding

QM QM

AMOEBA09 ONIOM(QM:AMOEBA09)

AMOEBA09


26

ONIOM(QM:AMOEBA09) Study on Binding Energies and Binding

Recommend Documents