Unstable, Metastable, or Stable Halogen Bonding Interaction Involving

Nov 12, 2014 - However, PDB survey revealed that 24% of the ligands with halogen bonding geometry could be negatively charged. Moreover, 36% of ...
0 downloads 0 Views 3MB Size
Subscriber access provided by DICLE UNIV

Article

Unstable, Meta-stable or Stable Halogen Bonding Interaction Involving Negatively Charged Donors? A Statistical and Computational Chemistry Study Zhuo Yang, Zhijian Xu, Yingtao Liu, Jinan Wang, Jiye Shi, Kaixian Chen, and Weiliang Zhu J. Phys. Chem. B, Just Accepted Manuscript • Publication Date (Web): 12 Nov 2014 Downloaded from http://pubs.acs.org on November 13, 2014

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 B 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 45

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

Unstable, Meta-stable or Stable Halogen Bonding Interaction Involving Negatively Charged Donors? A Statistical and Computational Chemistry Study Zhuo Yang, †, 1 Zhijian Xu, †,‡, 1 Yingtao Liu, † Jinan Wang, † Jiye Shi, †



§,*

Kaixian Chen,

and Weiliang Zhu †, *

Drug Discovery and Design Center, Key Laboratory of Receptor Research, State Key

Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China ‡

State Key Laboratory of Medicinal Chemical Biology, Nankai University

§

Informatics Department, UCB Pharma, 216 Bath Road, Slough SL1 4EN, United

Kingdom 1

These authors contributed equally to the work.

*

To whom correspondence should be addressed. Phone: +86-21-50805020, Fax:

+86-21-50807088, E-mail: [email protected], [email protected].

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

ABSTRACT The non-covalent halogen bonding could be attributed to the attraction between the positively charged σ-hole and a nucleophile. Quantum mechanics (QM) calculation indicated that the negatively charged organohalogens have no positively charged σ-hole on their molecular surface, leading to a postulation of repulsion between negatively charged organohalogens and nucleophile in vaccum. However, PDB survey revealed that 24% of the ligands with halogen bonding geometry could be negatively charged. Moreover, 36% of ionizable drugs in CMC (Comprehensive Medicinal Chemistry) are possibly negatively charged at pH 7.0. QM energy scan showed that the negatively charged halogen bonding is probably meta-stable in the vacuum. However, the QM calculated bonding energy turned negative in various solvents, suggesting that halogen bonding with negatively charged donors should be stable in reality. Indeed, QM/MM calculation on three crystal structures with negatively charged ligands revealed that the negatively charged halogen bonding was stable. Hence, we concluded that halogen bonding with negatively charged donors is unstable or meta-stable in the vacuum but stable in protein environment, and possesses similar geometric and energetic characteristics as conventional halogen bonding. Therefore, negatively charged organohalogens are still effective halogen bonding donors for medicinal chemistry and other applications.

KEYWORDS: Halogen bonding, Negatively charged organohalogens, Negatively charged halogen bonding, QM/MM

ACS Paragon Plus Environment

Page 2 of 45

Page 3 of 45

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

INTRODUCTION

Covalent-bonded halogens, especially heavy halogens (i.e. C–X, X = Cl, Br or I), display a positive electrostatic region along the extension of the covalent-bond, which is called the σ-hole; while the electrostatic potentials on the ring region perpendicular to the bond are usually negative.1-9 This anisotropy of charge distribution of halogen atoms has drawn much attention during past decades.7,

10-23

The non-covalent

attractive interaction between the σ-hole of halogen atoms and a nucleophile (i.e. Lewis base), viz. halogen bond (XB) has already shown practical value in a variety of fields, including crystal engineering,4,

6, 8, 11

polymer chemistry,10,

12, 24

inorganic

chemistry,4-6, 11 etc.

In medicinal chemistry, halogenation is one of the most common methods of molecular modification.25-28 In addition to traditional optimizations of molecules in the aspects of physical chemistry properties, e.g. increasing membrane permeability, facilitating the blood-brain barrier crossing and prolonging the lifetime of the drug, the introduction of heavy halogen atoms into drug molecules could also increase binding affinity remarkably by forming halogen bonds with target proteins analogous to hydrogen bond.15, 29-30

Studies have already shown the important role of halogen

bonding in hit identification and lead optimization, e.g. phosphodiesterase type 5 (PDE5) inhibitors,31 human Cathepsin L (hCatL) inhibitors, nicotinic acetylcholine receptor (nAChR) agonist,32 etc. Very recently, it was found that halogen bonds could contribute

to

the

binding

between

organohalogens and

ACS Paragon Plus Environment

plasma

transport

The Journal of Physical Chemistry

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

proteins/cytochrome P450/Glutathione S-transferases, indicating the contributions of halogen bonding to tuning ligand ADME/T property.33

To improve the binding affinity, highly electronegative or positively charged groups/moieties, e.g., nitro group or fluorine atom, could be introduced into oranohalogens to improve the electropositivity of the σ-hole.34 In addition, negatively charged acceptor could further enhance the halogen bonding strength.9, 35 For instance, the magnitude of the halogen bond C6F5I…Cl- can be as much as -23.80 kcal/mol (at MP2/aug-cc-pVDZ level).35 Nevertheless, most of the abovementioned studies only involved neutral organohalogens as halogen bonding donors.

In reality organohalogens including some drug molecules, could also be negatively charged. To the best of our knowledge, there is no systematic study about the interaction between a negatively charged organohalogen and heavy atoms like nitrogen and oxygen (called negative halogen bonding hereinafter). In particular, for the halogen bonding donors that deprotonate at physiological pH value, how would the negative net charge affect the normally positively charged σ-hole of the halogen atoms? Would the σ-hole still retain? Would these negatively charged molecules still form attractive interactions with nucleophiles? How prevalent is this type of interaction in PDB? Hence, it is of significance to perform a systematic study to explore the prevalence of the negatively charged molecules as halogen bonding donors and their effects on halogen bonding strength.

Here, we performed a study aiming to explore the potential effects of the

ACS Paragon Plus Environment

Page 4 of 45

Page 5 of 45

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

negatively charged donors on halogen bonding through the combined use of database survey, quantum mechanics and quantum mechanics/molecular mechanics (QM/MM) calculations. The survey revealed that the charged molecules accounted for more than half of the totality not only of the organohalogens in CMC, but also of the ligands that display halogen bonding geometry in the PDB. QM/MM calculations along with quantum mechanics-based energy scan revealed the similarities and differences between the typical halogen bonding and that with negatively charged donors, which could be of great value to further applications of halogen bonding in drug design and discovery.

MATERIALS AND METHODS

ESP on a molecular surface.

The electrostatic potential (ESP) V(r) around a

molecule can be calculated rigorously by,   = ∑ |

 

− |

 ′  ′  ′ 

,

(1)

where ZA is the charge on nucleus A, located at RA, and ρ(r) is the molecule’s electronic density. V(r) is a physical observable which can be determined both experimentally using diffraction techniques, and computationally. Its sign in any region of space depends upon whether the positive contribution of the nuclei or the negative contribution of the electrons is dominant. When plotted on the surface of a molecule (electron density ρ = 0.001 au) ,36 V(r) is designated VS(r) and its local most positive and most negative values (of which there may be several) are identified as VS,max and VS,min. In this study, VS(r), VS,max and VS,min were calculated by Multiwfn

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

(version: 3.2) .37

Database survey for negatively charged organohalogens. The CMC and the PDB were applied for the statistical analysis of negatively charged halogenated molecules at physiological pH value. The CMC is updated by Accelrys annually with compounds appearing in the United States Approved Names (USAN) list for the first time (1900 ~ present), thus covers most of the launched drugs. The 9,288 compounds in the CMC (version 2011.2) were exported in sdf format. Inorganic salts and very large molecules (molecular weight > 1000) were stripped off using Pipeline Pilot 7.5.30 After the remaining compounds were converted into three-dimensional structures in mol2 format by SYBYL 6.8,29 the Epik module34, 38-39 in Schrödinger 2010 software suite was applied to predict the protonation status at pH 7.0.

Crystal structures with two types of halogen bonds in the PDB were surveyed: C−X···Y and C−X···π (Figure 1).26, 40-42 For C−X···Y halogen bond, Y represents O, N or S with the intermolecular X···Y distances shorter than the sums of vdW radii (d(Cl···O) < 3.27 Å, d(Br···O) < 3.37 Å, d(I···O) < 3.50 Å, d(Cl···N) < 3.30 Å, d(Br···N) < 3.40 Å, d(I···N) < 3.53 Å, d(Cl···S) < 3.55 Å, d(Br···S) < 3.65 Å, d(I···S) < 3.78 Å) and the C–X···Y angles larger than 140°.26 For C−X···π halogen bond, π systems from aromatic residues (Phe, Tyr, His, and Trp) were considered when they satisfy the following criteria: d(Cl⋅⋅⋅π) < 4.2 Å, d(Br⋅⋅⋅π) < 4.3 Å, d(I⋅⋅⋅π) < 4.5 Å, α < 60° and θ > 120°.26 All the small molecules forming halogen bonds with proteins were exported in sdf format without hydrogen atoms. The LigPrep module40 in

ACS Paragon Plus Environment

Page 6 of 45

Page 7 of 45

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

Schrödinger 2010 software suite was then applied to add hydrogen atoms and to predict the protonation status at pH 7.0.

Figure 1. Two types of halogen bonds in PDB, viz. (a) C−X···Y and (b) C−X···π. QM/MM calculation. To explore the possible halogen bonds between negatively charged organohalogens and proteins, a two-layer ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) method43-45 was adopted for the QM/MM calculation of halogen bonds in the crystal structures. 3N5J,46 1P5E47 and 3JZB48 were selected as model systems with negatively charged molecules containing Cl, Br and I, respectively.

The ligands in the three crystal structures were predicted to be deprotonated by LigPrep and PROPKA (version: 3.1)49-52 at the pH values of the crystallization (Tables S1 & S2, Supporting Information). Only the protein monomers which form halogen bonds with the ligands were kept for the QM/MM calculations. The pKa values of ionizable residues in the proteins were calculated by H++ website42, 53-55 at the pH values of the crystallization and hydrogen atoms were added accordingly. The ligands and the corresponding protein backbones that form halogen bonds were

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 45

included in the QM region (Figure 4) which was described at the M06-2X/LanL2DZ level of density functional theory (DFT) for 3JZB and at the M06-2X/6-311++G** level for 3N5J and 1P5E.33 The rest part of the proteins was treated as the MM layer of the system and described by the AMBER parm96 force field.56

The QM/MM optimization was carried out without any constrains in the vacuum. The QM layer of the model was then extracted for single-point energy calculation at the MP2/aug-cc-pVDZ level, while Stuttgart/Dresden pseudopotential (SDD) basis set was adopted for iodine atoms in 3JZB.31, 57-59 The binding energies between the ligands and the protein backbones were assessed from equation (2).

∆ =  −  +   + 



(2)

where ∆E is the binding energy, Ecom is the energy of the complex, Edonor and Eacpt are the energies of the donor and the acceptor molecule, respectively, and BSSE stands for the basis set superposition error corrections.60 All these calculations were carried out with Gaussian 09 suite of programs.61

Quantum Mechanics-Based Grid Scan. The halogen bond distance and angle can be described distinctly by quantum mechanics-based grid scan from the aspect of interaction energy. The model molecules chosen as the halogen bond donors are electric neutral halobenzenes (phX, X = Cl, Br, I) and 4-halo-benzoic acids (p-CO2--phX, X = Cl, Br, I), which are electronegative at physiological pH value; the acceptor molecule is N-methylacetamide (BB) in order to mimic the protein backbone.23

ACS Paragon Plus Environment

Page 9 of 45

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

The geometry of every model complex was fully optimized with the acceptor atom (carbonyl oxygen) restricted in the plane of benzene and the plane of BB perpendicular to that of benzene (Figure S1) at the M06-2X level of theory,62 which has been reported to give good performance on the optimization of the halogen bond complexes.9, 26, 62-65 The SDD basis set was employed for iodine, whereas for other atoms aug-cc-pVDZ was applied.57, 59 Based on the optimized geometry, the halogen bond distance (d(X···O)) was scanned every 0.1 Å from 2.9 Å to 4.0 Å, and every 0.5 Å between 4.0 Å and 10.0 Å; meanwhile, the halogen bond angle (∠(C-X···O)) was scanned every 5° from 120° to 180°. Single-point energy calculations of the complex and each monomer were carried out at every point of grid, and the interaction energies including basis set superposition error (BSSE) corrections were assessed from equation (2). The grid scan in different solvents was carried out using the conductor-like polarizable continuum model (CPCM).66 The interaction energies evaluated in solvent was assessed from equation " " " ∆ = ! − _$! + !_$! 

(3)

Superscript S represents energy with solvent effect. Subscript A_bAB means energy of monomer A calculated with the whole basis functions of dimer AB, where atoms of monomer B were treated as ghost atoms. In this way, we can obtain the BSSE corrected interaction energy with solvent effect. All these calculations were carried out with Gaussian 09 suite of programs. RESULTS AND DISCUSSION

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 45

ESP of neutral and negatively charged organohalogens. In order to explore the potential effect of the negative charge on the σ-hole of halogen atoms, VS,max values of the halogen atoms were calculated in vacuum(Figure 2).

Figure 2. Electrostatic potentials mapped on the molecular surface (electron density ρ = 0.001 au) of (a) halogenobenzenes; (b) 4-fluo-halogenobenzenes; (c) 4-halo-anilines; (d) 4-halo-benzoic acids; (e) 4-halo-benzoates. As

expected,

for

neutral

organohalogens

(phX,

X

=

Cl,

Br,

I),

electron-withdrawing groups such as fluorine atom (p-F-phX, X = Cl, Br, I) or carboxyl group (p-CO2H-phX, X = Cl, Br, I) enhance the σ-hole (Figures 2b & d), resulting a more positive VS,max (Table 1); while electron-donating groups, e.g. the amino group (p-NH2-phX, X = Cl, Br, I), induce a smaller σ-hole (Figure 2c) and a less positive VS,max (Table 1). However, when the 4-halobenzoic acids are deprotonated (p-CO2--phX, X = Cl, Br, I), the electrostatic potentials all over the molecular surface turn negative. In other words, there is no conventional positively charged σ-hole existing on halogen atoms.

ACS Paragon Plus Environment

Page 11 of 45

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

The corresponding VS,max values were negative (Table 2), indicating possible repulsive X···Y/π interactions. However, the calculated potentials also show that the region of previous σ-hole displays less negative electrostatic potentials than other region with the order Cl < Br < I (Figure 2e & Table 2)

The interaction energy of neutral and negative halogen bonding. The correlation of ∆E with the VS,max of the halogen σ-hole has been demonstrated multiple times.6, 8-9 So the negative VS,max of the halogen σ-hole of deprotonated 4-halobenzoic acids suggested a positive interaction energy. To verify this inference, quantum chemistry optimization of halogen bonding complexes of the organohalogens with ammonia (NH3) as the acceptor were carried out in the vacuum; the interaction energies (∆E) of optimized complexes were then calculated (Tables 1 & 2).

For the neutral halogen bonding complexes, all the optimizations terminated in a typical halogen bonding geometry and most of them displayed an optimal linear interaction except for the p-NH2-phCl···NH3 (Table 1). The hydrogen atoms of ammonia in the optimized complex of p-NH2-phCl···NH3 have short interaction distances to chlorine (Figure S2), thus could interact with the chlorine, resulting a more negative interaction energy, although the VS,max the σ-hole on the chlorine is almost zero. Apart from this complex, other linear complexes do show a good correlation (R2 = 0.95) of ∆E with the VS,max of the halogen σ-hole (Figure S3).

Table 1. The VS,max on halogen atoms, geometrical parameters and interaction energy

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 12 of 45

(∆E) of optimized model organohalogens with NH3. phX p-F-phX X VS,maxa

Dopt

b

Aopt

c

d

∆E

VS,max Dopt

Aopt

p-NH2-phX VS,max Dopt

∆E

Aopt

∆E

Cl

4.33

3.14 180.0 -0.78

6.72

3.13 178.4 -1.00

0.58

3.17 160.7 -0.90

Br

8.36

3.13 179.6 -1.82

10.84 3.12 179.7 -2.08

4.74

3.15 179.7 -1.50

I

19.98

3.14 179.9 -3.59

22.53 3.11 179.9 -3.96

16.50 3.16 179.7 -3.25

a

b

c

Values are in kcal/mol. Values are in angstrom. Values are in degree. d Values are in kcal/mol. For the negative halogen bonding system in the vacuum, the optimization of 4-bromobenzoate and 4-chlorobenzoate with NH3 could not end in a halogen bonding geometry, suggesting that the negative halogen bonding between ammonia and 4-bromobenzoate or 4-chlorobenzoate is unstable. This result is expected and is in agreement with the calculated negative VS,max of the halogen σ-holes. However, 4-iodobenzoate could form a weak attractive halogen bonding interaction with NH3, which may be on account of the strong polarizability of the iodine atom, although the VS,max of the iodine atom was also negative. For the unstable halogen bonding, single point energy calculation with fixed geometry (viz. d(X···N) = 3.2 Å and ∠C–X···N = 180°) resulted in a positive energy, implying again a repulsive interaction (Table 2). Accordingly, the interaction involving negatively charged donors seems to be unstable in the vacuum. Table 2. The VS,max on halogen atoms, geometrical parameters and interaction energy (∆E) of optimized 4-halo-benzoic acids with NH3 in different protonation states. p-CO2--phX p-CO2H-phX X VS,maxa Doptb Aoptc ∆Ed VS,max Dopt Aopt ∆E e Cl 8.85 3.12 178.5 -1.23 -48.06 1.73f

a

Br

12.73

3.11

179.8

-2.31

-43.79

-

-

1.02f

I

24.30

3.10

179.8

-4.20

-32.84

3.30

179.9

-0.31

b

c

d

Values are in kcal/mol. Values are in angstrom. Values are in degree. Values are

ACS Paragon Plus Environment

Page 13 of 45

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

in kcal/mol. e Optimization could not terminate in a typical halogen bonding geometry. f Single point energy interacting with NH3 when d(X···N) = 3.2 Å and ∠C–X···N = 180°. Halogenated drugs with negative charges. To investigate how prevalent the negatively charged molecules with heavy halogens are in drugs, the CMC database was surveyed.

Out of the 9,288 compounds, 8,714 are chemical drugs, in which 2,263 contain halogen atoms (F, Cl, Br and I) and 1,571 can act as halogen bond donors (Figure 3a, Table S3). At pH 7.0, only 43% molecules in the CMC retained neutral, whlie 51% molecules with heavy halogen atoms are charged. Among the ionizable drugs with heavy halogen atoms, 36% are negatively charged. Therefore, the potential interaction between the negatively charged organohalogen drugs and their target, namely negative halogen bonding, is of significance for understanding drug-target interactions.

Figure 3. Proportions of organohalogens at different charge states in (a) the CMC and (b) the PDB with potential halogen bonding interaction.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 45

Searching for negative halogen bonding in PDB. The PDB was surveyed to validate the potential halogen bonding between negatively charged organohalogens and biomacromolecules. The current PDB (April 2014 release) contains 4,913 complex structures in which ligands are halogenated, among which 2,893 structures contain heavy organohalogens. Filtering these structures by the halogen geometry criteria resulted in 1,498 halogen bonds presented in 907 structures which corresponding to 1,322 small molecules (Table S4).

As we discussed previously, negatively charged organohalogens could barely form an attractive interaction as a halogen bonding donor in the vacuum. Noticeably, 24%

of

the

1,322

ligands

showing

halogen

bonding

geometry

with

biomacromolecules would deprotonate at pH7.0, resulting in negative net charge (Figure 3b and Table S4). This observation suggests that the negative halogen bonding geometry is prevalent in the PDB. In addition, a detailed analysis revealed that there are 3 ~ 10 intervening atoms (topology distance) between the halogen and the anionic oxygen in PDB, with a peak at 5 intervening atoms. The corresponding physical distances are 3.6 ~ 8 Å, with a peak at 6 ~ 8 Å (Figure S4). QM/MM calculations were then carried out to investigate whether these negative halogen bonding interactions in crystals are attractive and whether they contribute to the binding affinity of drug to target.

QM/MM calculation of the negative halogen bonding energy. 3N5J, 1P5E and 3JZB were selected as model systems for halogen bonding involved with negatively

ACS Paragon Plus Environment

Page 15 of 45

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

charged ligands containing Cl, Br and I, respectively. The model systems with at most 5 intervening atoms between the halogen and the anionic oxygen and a physical distance of ~6 Å thus represent the most frequent situation of the ligands in the PDB survey (Figure S4). Superposition of the heavy atoms in the QM layer in the crystal structures and the QM/MM optimized structures resulted in RMSDs of 1.45 Å, 0.74 Å and 0.88 Å for 3N5J, 1P5E and 3JZB, respectively (Figure 4). The deviations of X···O distances of the halogen bonds between crystal and optimized structures were less than 0.1 Å, and the deviations of C–X···O angles were less than 10° (Table 3), indicating that the results of the QM/MM optimization were reliable.

Figure 4. Optimized structures of the full models at the ONIOM level for (a) 3N5J (M06-2X/6-311++G**); (b) 1P5E (M06-2X/6-311++G**) and (c) 3JZB (M06-2X/LanL2DZ). Atoms in the QM layer are presented as balls and sticks with carbon atoms in yellow for ligands and gray for proteins; hydrogen atoms in white, oxygen atoms in red, nitrogen atoms in blue, chloride atoms in green, bromine atoms in brown and iodine atoms in purple. Atoms in the MM layer are shown as cartoon. As for the 3 deprotonated ligands, the calculated ESP mapped on the whole molecular surface (electron density ρ = 0.001) are negative (Figure 5), which is similar to the model systems in the vacuum (Figure 2e). ESP is also less negative on the surface around the conventional σ-hole region.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 45

Figure 5. Electrostatic potentials mapped on the molecular surface (electron density ρ = 0.001 au) of ligands: (a) 3N5J, (b) 1P5E and (c) 3JZB. Table 3. Geometrical parameters of halogen bonds in the model systems in crystal and QM/MM optimized structures. Crystal Structure QM/MM Optimized Structure X PDB Acceptor ID Atom d(X···O) (Å) ∠C–X···O (°) d(X···O) (Å) ∠C–X···O (°) Cl

3N5J

O(Ser205)

2.95

164.4

3.02

159.1

Br

1P5E

O(Glu81) O(Leu83)

3.01 2.90

168.5 164.7

2.99 2.82

166.5 171.3

3JZB O(Phe218)

3.22

169.6

3.12

173.5

I

Different from the model systems (Table 2), the X···O distances and C–X···O angles in the three QM/MM optimized negative halogen bonding structures are around 2.8 ~ 3.1 Å and 159~174˚, representing a typical halogen bonding geometry in comparison with conventional halogen bonding. Therefore, the negative halogen bonding in crystal structures might be attractive interaction. Indeed, the interaction

ACS Paragon Plus Environment

Page 17 of 45

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

energies between the halogen donor and acceptor in the QM layer calculated in the vacuum are 2.65 kcal/mol, -1.09 kcal/mol and -0.58 kcal/mol for 3N5J, 1P5E and 3JZB, respectively (Table 4). The positive binding energy of the chlorinated ligand and the protein backbone, as well as no VS,max on the chlorine atom of the ligand when ESPs were calculated with three positively charged amino acids (Lys57, Arg60 and Lys257) in the vicinity (Figure S5) in 3N5J, implies a probably repulsive interaction between

the chlorine and the oxygen atom. Although the negative binding energies for other two systems (1P5E and 3JZB) suggest an attractive binding, the strength is obviously weak in comparison with -2 ~ -4 kcal/mol between electrostatically neutral halogenated ligand and protein residues. 6, 9, 13, 26, 31 Nevertheless, the negative halogen bonding is possible to be attractive, which is different from our previous understanding and results calculated from the model systems in the vacuum (Table 2), suggesting that the environment may have significant effect on the negative halogen bonding interaction. Table 4. Interaction energies of QM layer in QM/MM optimized structures of the model systems in the vacuum, chloroform (ε = 4.71), acetone (ε = 20.49) and water (ε = 78.36). QM/MM Optimized Structure PDB Acceptor X ID Atom ∆Evacuum ∆Echloroform ∆Eacetone ∆Ewater Cl

3N5J

O(Ser205)

2.67

-0.023

-0.74

-0.91

Br

1P5E

O(Glu81) O(Leu83)

-1.09

-4.09

-4.95

-5.15

I

3JZB

O(Phe218)

-0.58

-2.69

-3.34

-3.50

The effect of dielectric constant on the negative halogen bonding. The local

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

dielectric of the protein binding site around ligands is inhomogeneous.67-68 In calculations, the dielectric properties of the protein and solvent phase are represented in terms of dielectric constant (ε).69 In general, the dielectric constant can be as little as 4~5 in the protein interior and as high as approximately 80 in the vicinity of the protein surface.67-71 For the above three model systems, the ligand in 3JZB is completely buried in the protein, while ligands in the other two are located in the binding sites accessible to water molecules. We calculated the interaction energies of the optimized QM layer in various solvents with different dielectric constant, viz., chloroform (ε = 4.71), acetone (ε = 20.49) and water (ε = 78.36), respectively (Table 4). Interestingly, the calculated binding energies are all negative for the 3 systems, indicating that the negative halogen bonding are attractive in all the 3 solvents. Surprisingly, it is observed that the binding energies grow stronger as the dielectric constant increases (Table 4), suggesting that negative halogen bonding is stable in the real biological environment.

Halogen bonding interaction energy versus dielectric constants. To further investigate the characteristics of the negative halogen bonding, we performed quantum mechanics-based energy scans in the vacuum and in different solvents using the complexes formed by neutral or negatively charged organohalogens and N-methylacetamide (BB) as model systems. Figure 6 depicts the scanned energy landscapes in the vacuum, demonstrating that neutral halogen bonding systems (halobenzene-BB complexes) have apparent negative energy well with strongest binding energy of -1.36, -2.44 and -4.12 kcal/mol for chlorobenzene-, bromobenzene-

ACS Paragon Plus Environment

Page 18 of 45

Page 19 of 45

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

and iodobenzene-BB systems, respectively (Fiugres 6a-c & Tables S5-7 in Supporting Information). Differently, although the scanned interaction energy profiles of the three negative halogen bonding systems (halobenzonate-BB complexes) are very similar in shape to those of the neutral systems, the lowest binding energy are +1.57, +0.81 and -0.34 kcal/mol for 4-chlorobenzoate-, 4-bromobenzoate- and 4-iodobenzoate-BB systems, respectively (Figures 6d-f & Tables S8-10), demonstrating that 4-chlorobenzoate- and 4-bromobenzoate-BB interactions are always repulsive at all the scanned angles and distances, while 4-iodobenzoate-BB interaction could be attractive when the interaction distance is around 3.3±0.2 Å and the angle around 180±10˚. Scans of the interaction energy for the halobenzonate-ammonia model systems in the vacuum resulted in similar interaction energy landscapes, with the lowest binding energy +1.56, +0.88 and -0.31 kcal/mol for 4-chlorobenzoate-, 4-bromobenzoate- and 4-iodobenzoate-NH3 systems, respectively (Tables S11-13 in Supporting Information). Nevertheless, the scanned interaction energy profiles for the negative halogen bonding systems reveal the existence of energy well with interaction distance of 3.3±0.2 Å and angle 180˚, suggesting that meta-stable structures do exist for the negative halogen bonding systems.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Figure 6. Illustration of grid-scans of interaction energies in the vacuum between (a) chlorobenzene (phCl); (b) bromobenzene (phBr); (c) iodobenzene (phI); (d) 4-chlorobenzoate (p-CO2--phCl); (e) 4-bromobenzoate (p-CO2--phBr); (f) 4-iodobenzoate (p-CO2--phI) and N-methylacetamide (BB) with the change in X···O distance and C–X···O angle. As 180° is the optimal angel of ∠ (C-X···Y) for interaction between BB and phX or p-CO2--phX in the vacuum, the interaction distance was further scanned to 10 Å for bromobenzene- and 4-bromobenzoate-BB systems. Figure 7 shows both systems do have apparent energy wells, but of different profiles. The energy wells have different depth (Figures 7b & d); the former is about 2.5 kcal/mol while the later about 0.7 kcal/mol. When the distance exceeds the optimal value, the energy of the neutral halogen bonding interaction goes uphill all the way until reaching a plateau (Figure 7b). On the contrary, an energy barrier is observed in the negative halogen bonding system (Figure 7d), suggesting that the interaction at 3.2 Å and 180° is a local minimum, thus, which corresponds to a meta-stable structure.

ACS Paragon Plus Environment

Page 20 of 45

Page 21 of 45

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

Figure 7. Illustration of grid-scan of interaction energies between (a) bromobenzene (phBr); (c) 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with the change in Br···O distance and C–Br···O angle. Curves of interaction energies between (b) bromobenzene (phBr); (d) 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with Br···O distance varying from 2.9 to 10.0 Å when C–Br···O angle fixed to 180°. Figure 8 illustrates the scanned interaction energy of the negative halogen bonding system in different environments using 4-bromobenzoate-BB as a model system. Interestingly, the meta-stable complex turns out to be stabilized in various solvents according to the calculated negative interaction energies. The optimal distance determined by the grid scan reduces from 3.2 Å in the vacuum to 3.1 Å for all the scan models with different solvents. With the increase of dielectric constant of the solvent, the lowest interaction energy for each scan model decreases (Figure 8, 9; Table S9, S14-S18), indicating that the negative halogen bonding is more stable in the

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

more polar environment. Indeed, proteins could provide an inhomogeneous polar environment to stabilize the negative halogen bonding.

Figure 8. Illustration of grid-scans of interaction energies between 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with the change in Br···O distance and C–Br···O angle in (a) the vacuum; (b) chloroform (ε = 4.71); (c) acetone (ε = 20.49); (d) methanol (ε = 32.61); (e) DMSO (ε = 46.83) and (f) water (ε = 78.36).

The above results of grid-scans may shed some lights on the negative halogen bonding. Although the σ-hole with negative potentials repulses the carbonyl oxygen of protein backbones, the interaction energy finds its local minimum at the typical halogen bonding geometry even in the vacuum. As the dielectric constant increases, the binding energies decrease to negative values for both QM/MM high layers and grid-scanned models, implying that the interactions become attractive and stable, which accounts for the result of our PDB survey.

ACS Paragon Plus Environment

Page 22 of 45

Page 23 of 45

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

Figure 9. Interaction energies between 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with Br···O distance varying from 2.9Å to 10.0 Å when C–Br···O angle fixed to 180° in (a) the vacuum; (b) chloroform (ε = 4.71); (c) acetone (ε = 20.49); (d) methanol (ε = 32.61); (e) DMSO (ε = 46.83) and (f) water (ε = 78.36).

CONCLUSION

Molecules have different protonation states depending on their pKa and the pH value of the environment. Heavy-halogenated drugs that would deprotonate at the physiological pH value may display negative electrostatic potentials all over the molecular surface, but the previous electrostatically positive σ-hole of the halogen atom still presents less negative electrostatic potentials than that of the vicinity. The PDB survey demonstrates that negatively charged molecules could exhibit halogen bonding geometry similar to those electrostatically neutral molecules, which was supported by the QM/MM optimization results for three crystal structures (PDB ID: 3N5J, 1P5E and 3JZB). However, the interaction energies between the halogen-bonding donors and acceptors in the vacuum are higher than that of normal halogen bonding complex; the interactions could even become repulsive.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Quantum mechanics-based energy scan reveals that the interaction between an electrostatically negative donor and a normal acceptor with typical halogen bonding geometry is repulsive in the vacuum but with an energy well. When solvent models are applied, the interaction energies turn negative and the energy surfaces become similar to that of a conventional halogen bonding complex.

Charged drugs are common according to the CMC survey. Our study here demonstrates that, similar to electrostatically neutral molecules, negatively charged molecules with heavy halogen atoms can also form halogen bonds, which affirms the significant role of halogen bonding in drug discovery and development.

In addition, the grid-scan results also demonstrate that the interaction energy of halogen bonding between a negatively charged donor and a normal acceptor at the optimal point decreases with increasing dielectric constant. The similar phenomenon was observed by Zhang etc. on the arginine−arginine (Arg-Arg) pairing.72 Whether the solvation effects and electrostatic energies contribute significantly to the stability of halogen bonding involving negatively charged donors in the way similar as their roles in Arg-Arg pairing requires further investigation.

Supporting Information Available: Illustration of quantum mechanics-based scan. Optimized structures of non-linear and linear halogen-bonding complexes. Plot of interaction energies (∆E) with VS,max of halogen σ-hole for halogen-bonding complexes. Calculated pKa value and details of the ligand in the protein environment by PROPKA. Frequency of the topology distances and corresponding physical

ACS Paragon Plus Environment

Page 24 of 45

Page 25 of 45

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

distances between the halogen and the anionic oxygen of the ligand that halogen bonding with proteins in PDB. VS,max and VS,min of the ligand with positive charged animo acids in the vicinity (Lys57, Arg60 and Lys257) in QM/MM optimized structure of 3N5J. Organohalogens with different charged states in CMC. Organohalogens with different charged states that form halogen bonds with biomacromolecules in PDB (Protein Data Bank). Grid-scan of interaction energies (kcal/mol) between halobenzene (phX, X = Cl, Br, I) and N-methylacetamide (BB) with the change in X··O distance (A) and C–X···O angle (°) in the vacuum. Grid-scan of interaction energies (kcal/mol) between 4-halo-benzoate (p-CO2--phX, X = Cl, Br, I) and N-methylacetamide (BB) with the change in X···O distance (A) and C–X···O angle (°) in the vacuum. Grid-scan of interaction energies (kcal/mol) between 4-halo-benzoate(p-CO2--phX, X = Cl, Br, I) and ammonia (NH3) with the change in X···N distance (A) and C–X···N angle (°) in the vacuum. Grid-scan of interaction energies (kcal/mol) between 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with the change in Br···O distance (A) and C–Br···O angle (°) in chloroform (ε = 4.71), acetone (ε = 20.49), methanol (ε = 32.61), DMSO (ε = 46.83) and water (ε = 78.36). The material is available free of charge via the Internet at http://pubs.acs.org.

ACKNOWLEDGMENT

This work was supported by NNSF (81273435 and 81302699), National Science & Technology Major Project (2013ZX09103001-001 and 2012ZX09301-001-004), Ministry of Science and Technology (2012AA01A305 and 2012AA020302) and the

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

State Key Laboratory of Medicinal Chemical Biology, Nankai University (20130265).

REFERENCES (1) Clark, T.; Hennemann, M.; Murray, J.; Politzer, P. Halogen Bonding: The σ-Hole. J. Mol. Model. 2007, 13 (2), 291-296. (2) Hennemann, M.; Murray, J. S.; Politzer, P.; Riley, K. E.; Clark, T. Polarization-Induced Sigma-Holes and Hydrogen Bonding. J. Mol. Model. 2012, 18 (6), 2461-2469. (3) Huber, S. M.; Jimenez-Izal, E.; Ugalde, J. M.; Infante, I. Unexpected Trends in Halogen-Bond Based Noncovalent Adducts. Chem. Commun. (Cambridge, U.K.) 2012, 48 (62), 7708-7710. (4) Legon, A. C. The Halogen Bond: An Interim Perspective. Phys. Chem. Chem. Phys. 2010, 12 (28), 7736-7747. (5) Metrangolo, P.; Resnati, G. Chemistry. Halogen Versus Hydrogen. Science 2008, 321 (5891), 918-919. (6) Politzer, P.; Lane, P.; Concha, M. C.; Ma, Y.; Murray, J. S. An Overview of Halogen Bonding. J. Mol. Model. 2007, 13 (2), 305-311. (7) Politzer, P.; Murray, J. S.; Clark, T. Halogen Bonding: An Electrostatically-Driven Highly Directional Noncovalent Interaction. Phys. Chem. Chem. Phys. 2010, 12 (28), 7748-7757. (8) Politzer, P.; Murray, J. S. Halogen Bonding: An Interim Discussion.

ACS Paragon Plus Environment

Page 26 of 45

Page 27 of 45

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

ChemPhysChem 2013, 14 (2), 278-294. (9) Politzer, P.; Murray, J. S.; Clark, T. Halogen Bonding and Other Sigma-Hole Interactions: A Perspective. Phys. Chem. Chem. Phys. 2013, 15 (27), 11178-11189. (10) Metrangolo, P.; Resnati, G. Halogen Bonding: A Paradigm in Supramolecular Chemistry. Chemistry 2001, 7 (12), 2511-2519. (11) Metrangolo, P.; Neukirch, H.; Pilati, T.; Resnati, G. Halogen Bonding Based Recognition Processes: A World Parallel to Hydrogen Bonding. Acc. Chem. Res. 2005, 38 (5), 386-395. (12) Metrangolo, P.; Meyer, F.; Pilati, T.; Resnati, G.; Terraneo, G. Halogen Bonding in Supramolecular Chemistry. Angew. Chem., Int. Ed. 2008, 47 (33), 6114-6127. (13) Lu, Y.; Shi, T.; Wang, Y.; Yang, H.; Yan, X.; Luo, X.; Jiang, H.; Zhu, W. Halogen Bonding--a Novel Interaction for Rational Drug Design? J. Med. Chem. 2009, 52 (9), 2854-2862. (14) Zhou, P.; Lv, J.; Zou, J.; Tian, F.; Shang, Z. Halogen-Water-Hydrogen Bridges in Biomolecules. J. Struct. Biol. 2010, 169 (2), 172-182. (15) Hardegger, L. A.; Kuhn, B.; Spinnler, B.; Anselm, L.; Ecabert, R.; Stihle, M.; Gsell, B.; Thoma, R.; Diez, J.; Benz, J., et al. Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions. Angew. Chem., Int. Ed. 2011, 50 (1), 314-318. (16) Ibrahim, M. A. Molecular Mechanical Study of Halogen Bonding in Drug Discovery. J. Comput. Chem. 2011, 32 (12), 2564-2574. (17) Carlsson, A. C.; Grafenstein, J.; Budnjo, A.; Laurila, J. L.; Bergquist, J.; Karim,

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

A.; Kleinmaier, R.; Brath, U.; Erdelyi, M. Symmetric Halogen Bonding Is Preferred in Solution. J. Am. Chem. Soc. 2012, 134 (12), 5706-5715. (18) Erdelyi, M. Halogen Bonding in Solution. Chem. Soc. Rev. 2012, 41 (9), 3547-3557. (19) Ibrahim, M. A. Molecular Mechanical Perspective on Halogen Bonding. J. Mol. Model. 2012, 18 (10), 4625-4638. (20) Zhou, P.; Huang, J.; Tian, F. Specific Noncovalent Interactions at Protein-Ligand Interface: Implications for Rational Drug Design. Curr. Med. Chem. 2012, 19 (2), 226-238. (21) Pinter, B.; Nagels, N.; Herrebout, W. A.; De Proft, F. Halogen Bonding from a Hard and Soft Acids and Bases Perspective: Investigation by Using Density Functional Theory Reactivity Indices. Chemistry 2013, 19 (2), 519-530. (22) Scholfield, M. R.; Zanden, C. M.; Carter, M.; Ho, P. S. Halogen Bonding (X-Bonding): A Biological Perspective. Protein Sci. 2013, 22 (2), 139-152. (23) Wilcken, R.; Zimmermann, M. O.; Lange, A.; Joerger, A. C.; Boeckler, F. M. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology. J. Med. Chem. 2013, 56 (4), 1363-1388. (24) Rissanen, K. Halogen Bonded Supramolecular Complexes and Networks. CrystEngComm 2008, 10 (9), 1107-1113. (25) Kubota, H.; Avarbock, M. R.; Brinster, R. L. Growth Factors Essential for Self-Renewal and Expansion of Mouse Spermatogonial Stem Cells. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (47), 16489-16494.

ACS Paragon Plus Environment

Page 28 of 45

Page 29 of 45

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

(26) Lu, Y.; Wang, Y.; Zhu, W. Nonbonding Interactions of Organic Halogens in Biological Systems: Implications for Drug Discovery and Biomolecular Design. Phys. Chem. Chem. Phys. 2010, 12 (18), 4543-4551. (27) Merino, A.; Bronowska, A. K.; Jackson, D. B.; Cahill, D. J. Drug Profiling: Knowing Where It Hits. Drug Discov. Today 2010, 15 (17-18), 749-756. (28) Wilcken, R.; Liu, X.; Zimmermann, M. O.; Rutherford, T. J.; Fersht, A. R.; Joerger, A. C.; Boeckler, F. M. Halogen-Enriched Fragment Libraries as Leads for Drug Rescue of Mutant P53. J. Am. Chem. Soc. 2012, 134 (15), 6810-6818. (29) Lam, P. Y. S.; Clark, C. G.; Smallwood, A. M.; Alexander, R. S. Structure-Based Drug Design Utilizing Halogen Bonding: Factor Xa Inhibitors. In The 238th ACS National Meeting, Metrangolo, P.; Resnati, G., Eds. ACS: Washington, DC, 2009; p 58. (30) Auffinger, P.; Hays, F. A.; Westhof, E.; Ho, P. S. Halogen Bonds in Biological Molecules. Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (48), 16789-16794. (31) Xu, Z.; Liu, Z.; Chen, T.; Wang, Z.; Tian, G.; Shi, J.; Wang, X.; Lu, Y.; Yan, X.; Wang, G., et al. Utilization of Halogen Bond in Lead Optimization: A Case Study of Rational Design of Potent Phosphodiesterase Type 5 (PDE5) Inhibitors. J. Med. Chem. 2011, 54 (15), 5607-5611. (32) Rohde, L. A. H.; Ahring, P. K.; Jensen, M. L.; Nielsen, E. Ø.; Peters, D.; Helgstrand, C.; Krintel, C.; Harpsøe, K.; Gajhede, M.; Kastrup, J. S., et al. Intersubunit Bridge Formation Governs Agonist Efficacy at Nicotinic Acetylcholine Α4β2 Receptors: Unique Role of Halogen Bonding Revealed. J. Biol. Chem. 2012,

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

287 (6), 4248-4259. (33) Xu, Z.; Yang, Z.; Liu, Y.; Lu, Y.; Chen, K.; Zhu, W. Halogen Bond: Its Role Beyond Drug-Target Binding Affinity for Drug Discovery and Development. J. Chem. Inf. Model. 2014, 54 (1), 69-78. (34) Riley, K. E.; Murray, J. S.; Fanfrlik, J.; Rezac, J.; Sola, R. J.; Concha, M. C.; Ramos, F. M.; Politzer, P. Halogen Bond Tunability I: The Effects of Aromatic Fluorine Substitution on the Strengths of Halogen-Bonding Interactions Involving Chlorine, Bromine, and Iodine. J. Mol. Model. 2011, 17 (12), 3309-3318. (35) Lu, Y.; Li, H.; Zhu, X.; Zhu, W.; Liu, H. How Does Halogen Bonding Behave in Solution? A Theoretical Study Using Implicit Solvation Model. J. Phys. Chem. A 2011, 115 (17), 4467-4475. (36) Bader, R. F. W.; Carroll, M. T.; Cheeseman, J. R.; Chang, C. Properties of Atoms in Molecules: Atomic Volumes. J. Am. Chem. Soc. 1987, 109 (26), 7968-7979. (37) Lu, T.; Chen, F. Multiwfn: A Multifunctional Wavefunction Analyzer. J. Comput. Chem. 2012, 33 (5), 580-592. (38) Shelley, J. C.; Cholleti, A.; Frye, L. L.; Greenwood, J. R.; Timlin, M. R.; Uchimaya, M. Epik: A Software Program for pK(a) Prediction and Protonation State Generation for Drug-Like Molecules. J. Comput. Aided Mol. Des. 2007, 21 (12), 681-691. (39) Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the Comprehensive, Rapid, and Accurate Prediction of the Favorable Tautomeric States of Drug-Like Molecules in Aqueous Solution. J. Comput. Aided Mol. Des. 2010, 24

ACS Paragon Plus Environment

Page 30 of 45

Page 31 of 45

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

(6-7), 591-604. (40) Voth, A. R.; Ho, P. S. The Role of Halogen Bonding in Inhibitor Recognition and Binding by Protein Kinases. Curr. Top. Med. Chem. 2007, 7 (14), 1336-1348. (41) Forni, A.; Pieraccini, S.; Rendine, S.; Gabas, F.; Sironi, M. Halogen-Bonding Interactions

with

Pi

Systems:

CCSD(T),

MP2,

and

DFT

Calculations.

ChemPhysChem 2012, 13 (18), 4224-4234. (42) Matter, H.; Nazare, M.; Gussregen, S.; Will, D. W.; Schreuder, H.; Bauer, A.; Urmann, M.; Ritter, K.; Wagner, M.; Wehner, V. Evidence for C-Cl/C-Br...Pi Interactions as an Important Contribution to Protein-Ligand Binding Affinity. Angew. Chem., Int. Ed. 2009, 48 (16), 2911-2916. (43) 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. (44) Dapprich, S.; Komáromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. A New Oniom Implementation in Gaussian98. Part I. The Calculation of Energies, Gradients, Vibrational Frequencies and Electric Field Derivatives. J. Mol. Struct.–THEOCHEM 1999, 461–462 (0), 1-21. (45) Vreven, T.; Morokuma, K.; Farkas, O.; Schlegel, H. B.; Frisch, M. J. Geometry Optimization with Qm/Mm, Oniom, and Other Combined Methods. I. Microiterations and Constraints. J. Comput. Chem. 2003, 24 (6), 760-769.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

(46) Jahnke, W.; Rondeau, J. M.; Cotesta, S.; Marzinzik, A.; Pelle, X.; Geiser, M.; Strauss, A.; Gotte, M.; Bitsch, F.; Hemmig, R., et al. Allosteric Non-Bisphosphonate Fpps Inhibitors Identified by Fragment-Based Discovery. Nat. Chem. Biol. 2010, 6 (9), 660-666. (47) De Moliner, E.; Brown, N. R.; Johnson, L. N. Alternative Binding Modes of an Inhibitor to Two Different Kinases. Eur. J. Biochem. 2003, 270 (15), 3174-3181. (48) Martinez, L.; Nascimento, A. S.; Nunes, F. M.; Phillips, K.; Aparicio, R.; Dias, S. M.; Figueira, A. C.; Lin, J. H.; Nguyen, P.; Apriletti, J. W., et al. Gaining Ligand Selectivity in Thyroid Hormone Receptors Via Entropy. Proc. Natl. Acad. Sci. U.S.A. 2009, 106 (49), 20717-20722. (49) Li, H.; Robertson, A. D.; Jensen, J. H. Very Fast Empirical Prediction and Rationalization of Protein Pka Values. Proteins 2005, 61 (4), 704-721. (50) Bas, D. C.; Rogers, D. M.; Jensen, J. H. Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes. Proteins 2008, 73 (3), 765-783. (51) Olsson, M. H. M.; Søndergaard, C. R.; Rostkowski, M.; Jensen, J. H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions. J. Chem. Theory Comput. 2011, 7 (2), 525-537. (52) Søndergaard, C. R.; Olsson, M. H. M.; Rostkowski, M.; Jensen, J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values. J. Chem. Theory Comput. 2011, 7 (7), 2284-2295. (53) Gordon, J. C.; Myers, J. B.; Folta, T.; Shoja, V.; Heath, L. S.; Onufriev, A. H++: A Server for Estimating pKas and Adding Missing Hydrogens to Macromolecules.

ACS Paragon Plus Environment

Page 32 of 45

Page 33 of 45

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

Nucleic Acids Res. 2005, 33 (Web Server issue), W368-371. (54) Myers, J.; Grothaus, G.; Narayanan, S.; Onufriev, A. A Simple Clustering Algorithm Can Be Accurate Enough for Use in Calculations of pKs in Macromolecules. Proteins 2006, 63 (4), 928-938. (55) Anandakrishnan, R.; Aguilar, B.; Onufriev, A. V. H++ 3.0: Automating Pk Prediction and the Preparation of Biomolecular Structures for Atomistic Molecular Modeling and Simulations. Nucleic Acids Res. 2012, 40 (Web Server issue), W537-541. (56) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117 (19), 5179-5197. (57) Asaduzzaman, A.; Schreckenbach, G. Computational Study of the Ground State Properties of Iodine and Polyiodide Ions. Theor. Chem. Acc. 2009, 122 (3-4), 119-125. (58) Forni, A.; Rendine, S.; Pieraccini, S.; Sironi, M. Solvent Effect on Halogen Bonding: The Case of the Icdots, Three Dots, Centeredo Interaction. J. Mol. Graph. Model. 2012, 38, 31-39. (59) Yuan, K.; Liu, Y.; Zhu, Y.; Zuo, G.; Lü, L.; Li, Z. Theoretical Characterization of Single-Electron Iodine-Bond Weak Interactions in CH3…I-Y(Y = BH2, H, CH3, C2H3, C2H, CN, NC) Systems. Chin. Sci. Bull. 2012, 57 (4), 328-335. (60) Boys, S. F.; Bernardi, F. The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors. Mol.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Phys. 1970, 19 (4), 553-566. (61) M. J. Frisch; G. W. Trucks; H. B. Schlegel; G. E. Scuseria; M. A. Robb; J. R. Cheeseman; G. Scalmani; V. Barone; B. Mennucci; G. A. Petersson, et al. Gaussian 09, Revision C.01. Gaussian, Inc., Wallingford Ct. 2009. (62) Zhao, Y.; Truhlar, D. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theor. Chem. Acc. 2008, 120 (1-3), 215-241. (63) Takatani, T.; Sears, J. S.; Sherrill, C. D. Assessing the Performance of Density Functional Theory for the Electronic Structure of Metal−Salens: The M06 Suite of Functionals and the D4-Metals. J. Phys. Chem. A 2010, 114 (43), 11714-11718. (64) Kozuch, S.; Martin, J. M. L. Halogen Bonds: Benchmarks and Theoretical Analysis. J. Chem. Theory Comput. 2013, 9 (4), 1918-1931. (65) Esrafili, M. D. A Theoretical Investigation of the Characteristics of Hydrogen/Halogen Bonding Interactions in Dibromo-Nitroaniline. J. Mol. Model. 2013, 19 (3), 1417-1427. (66) Barone, V.; Cossi, M. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model. J. Phys. Chem. A 1998, 102 (11), 1995-2001. (67) Patargias, G. N.; Harris, S. A.; Harding, J. H. A Demonstration of the Inhomogeneity of the Local Dielectric Response of Proteins by Molecular Dynamics

ACS Paragon Plus Environment

Page 34 of 45

Page 35 of 45

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

Simulations. J. Chem. Phys. 2010, 132 (23), 235103. (68) Guest, W. C.; Cashman, N. R.; Plotkin, S. S. A Theory for the Anisotropic and Inhomogeneous Dielectric Properties of Proteins. Phys. Chem. Chem. Phys. 2011, 13 (13), 6286-6295. (69) Simonson, T.; Brooks, C. L. Charge Screening and the Dielectric Constant of Proteins:  Insights from Molecular Dynamics. J. Am. Chem. Soc. 1996, 118 (35), 8452-8458. (70) Nymeyer, H.; Zhou, H. X. A Method to Determine Dielectric Constants in Nonhomogeneous Systems: Application to Biological Membranes. Biophys. J. 2008, 94 (4), 1185-1193. (71) Simonson, T. What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed? J. Chem. Theory Comput. 2013, 9 (10), 4603-4608. (72) Zhang, Z.; Xu, Z.; Yang, Z.; Liu, Y.; Wang, J.; Shao, Q.; Li, S.; Lu, Y.; Zhu, W. The Stabilization Effect of Dielectric Constant and Acidic Amino Acids on Arginine-Arginine (Arg-Arg) Pairings: Database Survey and Computational Studies. J. Phys. Chem. B 2013, 117 (17), 4827-4835.

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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 TOC graphic 177x63mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 36 of 45

Page 37 of 45

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

Figure 1. Two types of halogen bonds in PDB, viz. (a) C-X•••Y and (b) C-X•••π. 177x139mm (300 x 300 DPI)

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Figure 2. Electrostatic potentials mapped on the molecular surface (electron density ρ = 0.001 au) of (a) halogenobenzenes; (b) 4-fluo-halogenobenzenes; (c) 4-halo-anilines; (d) 4-halo-benzoic acids; (e) 4-halobenzoates 220x114mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 38 of 45

Page 39 of 45

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

Figure 3. Proportions of organohalogens at different charge states in (a) the CMC and (b) the PDB with potential halogen bonding interaction. 254x190mm (300 x 300 DPI)

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Figure 4. Optimized structures of the full models at the ONIOM level for (a) 3N5J (M06-2X/6-311++G**); (b) 1P5E (M06-2X/6-311++G**) and (c) 3JZB (M06-2X/LanL2DZ). Atoms in the QM layer are presented as balls and sticks with carbon atoms in yellow for ligands and gray for proteins; hydrogen atoms in white, oxygen atoms in red, nitrogen atoms in blue, chloride atoms in green, bromine atoms in brown and iodine atoms in purple. Atoms in the MM layer are shown as cartoon. 254x67mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 40 of 45

Page 41 of 45

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

Figure 5. Electrostatic potentials mapped on the molecular surface (electron density ρ = 0.001 au) of ligands: (a) 3N5J, (b) 1P5E and (c) 3JZB. 169x194mm (300 x 300 DPI)

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Figure 6. Illustration of grid-scans of interaction energies in the vacuum between (a) chlorobenzene (phCl); (b) bromobenzene (phBr); (c) iodobenzene (phI); (d) 4-chlorobenzoate (p-CO2--phCl); (e) 4-bromobenzoate (p-CO2--phBr); (f) 4-iodobenzoate (p-CO2--phI) and N-methylacetamide (BB) with the change in X•••O distance and C–X•••O angle. 338x186mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 42 of 45

Page 43 of 45

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

Figure 7. Illustration of grid-scan of interaction energies between (a) bromobenzene (phBr); (c) 4bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with the change in Br•••O distance and C– Br•••O angle. Curves of interaction energies between (b) bromobenzene (phBr); (d) 4-bromobenzoate (pCO2--phBr) and N-methylacetamide (BB) with Br•••O distance varying from 2.9 to 10.0 Å when C–Br•••O angle fixed to 180°. 169x135mm (300 x 300 DPI)

ACS Paragon Plus Environment

The Journal of Physical Chemistry

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

Figure 8. Illustration of grid-scans of interaction energies between 4-bromobenzoate (p-CO2--phBr) and Nmethylacetamide (BB) with the change in Br•••O distance and C–Br•••O angle in (a) the vacuum; (b) chloroform (ε = 4.71); (c) acetone (ε = 20.49); (d) methanol (ε = 32.61); (e) DMSO (ε = 46.83) and (f) water (ε = 78.36). 338x186mm (300 x 300 DPI)

ACS Paragon Plus Environment

Page 44 of 45

Page 45 of 45

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

Figure 9. Interaction energies between 4-bromobenzoate (p-CO2--phBr) and N-methylacetamide (BB) with Br•••O distance varying from 2.9Å to 10.0 Å when C–Br•••O angle fixed to 180° in (a) the vacuum; (b) chloroform (ε = 4.71); (c) acetone (ε = 20.49); (d) methanol (ε = 32.61); (e) DMSO (ε = 46.83) and (f) water (ε = 78.36). 152x84mm (300 x 300 DPI)

ACS Paragon Plus Environment