Exchange of Cl+ between Lone-Pair Donors and π-Donors: A Computational Study

2000 ◽  
Vol 6 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Theis I. Sølling ◽  
Leo Radom
Keyword(s):  
Ab Initio ◽  
Computational Study ◽  
Lone Pair ◽  
Binding Energies ◽  
Lewis Base ◽  
Molecular Orbital Calculations ◽  
Reaction Energy ◽  
Lewis Bases ◽  
Donor Ability ◽  
Reaction Energies

The chemistry of mono-adducts ([Cl–X]+) between Cl+ and a Lewis base (X = NH3, H2O, HF, PH3, H2S or HCl) has been investigated using ab initio molecular orbital calculations at the G2 level. The reactions of such mono-adducts with additional Lewis bases (Y) are found to give [Y–Cl]+ plus X, generally without an intermediate barrier, via a bis-adduct [Y–Cl–X]+. The binding energies of the bis-adduct and the reaction energies are related to the donor properties of the Lewis bases. The reactions between the mono-adducts [Cl–X]+ and the π-donors ethylene and acetylene yield chloriranium and chlorirenium ions, respectively. These reactions proceed via complexes that resemble either the reactants or products depending on the sign of the reaction energy, the latter in turn being determined by the donor ability of the Lewis base. Results for the chlorine systems are compared with those for the corresponding phosphorus systems investigated previously.

scholarly journals Anion Recognition by Neutral and Cationic Iodotriazole Halogen Bonding Scaffolds

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 798
Author(s):  
Iñigo Iribarren ◽  
Goar Sánchez-Sanz ◽  
Cristina Trujillo
Keyword(s):  
Density Functional ◽  
Computational Study ◽  
Halogen Bond ◽  
Anion Recognition ◽  
Lone Pair ◽  
Halogen Bonding ◽  
Binding Energies ◽  
Bond Critical Point ◽  
Density Values ◽  
Intramolecular Hydrogen

A computational study of the iodide discrimination by different neutral and cationic iodotriazole halogen bonding hosts was carried out by means of Density Functional Theory. The importance of the size of the scaffold was highlighted and its impact observed in the binding energies and intermolecular X⋯I distances. Larger scaffolds were found to reduce the electronic repulsion and increase the overlap between the halide electron lone pair and the corresponding I-C antibonding orbital, increasing the halogen bonding interactions. Additionally, the planarity plays an important role within the interaction, and can be tuned using hydroxyl to perform intramolecular hydrogen bonds (IMHB) between the scaffold and the halogen atoms. Structures with IMHB exhibit stronger halogen bond interactions, as evidenced by the shorter intramolecular distances, larger electron density values at the bond critical point and more negative binding energies.

scholarly journals GAS PHASE STRUCTURE AND STABILITY OF COMPLEX FORMED BY H2O, NH3, H2S AND THEIR METHYL DERIVATIVES WITH THE CATION CO2+

2010 ◽  
Vol 4 (2) ◽  
pp. 106-109
Author(s):  
Cahyorini Kusumawardani
Keyword(s):  
Ab Initio ◽  
Gas Phase ◽  
Complex Structure ◽  
Cobalt Complex ◽  
Binding Energies ◽  
Structure Stability ◽  
Molecular Orbital Calculations ◽  
Hartree Fock ◽  
Methyl Derivatives ◽  
Gas Phase Structure

Ab initio molecular orbital calculations at the Hartree-Fock-Self Consistent Field (HF-SCF) have been performed in order to determine the structure and gas phase energies of complex formed by the Lewis bases of H2O, NH3, H2S and their methyl derivatives with the cation Co2+. The relative basicities of the base studied depend on both the substituent. The gas-phase interaction energies computed by the SCF method including electron correlation Møller-Plesset 2 (MP2) dan Configuration Iteration (CI) were comparable in accuracy. The binding energies computed by these two methods reach the targeted chemical accuracy.   Keywords: ab initio calculation, cobalt complex, structure stability

Changing Partners: Complex Substitution

Reactions ◽  
2011 ◽  
Author(s):  
Peter Atkins
Keyword(s):  
Metal Atom ◽  
Lewis Acid ◽  
Periodic Table ◽  
Noble Metals ◽  
Lone Pair ◽  
Lewis Base ◽  
Central Metal Atom ◽  
Important Special Case ◽  
Lewis Bases ◽  
Special Case

I shall now describe a special case of the Lewis acid–base reactions I introduced in Reaction 9. I showed there that a Lewis acid is a species that can accept a lone pair from another incoming species and form a bond to it, that a Lewis base is a species that provides that lone pair, and that the result of this sharing is a complex of the two species joined together by a chemical bond. The important special case I would like to share with you here is when the Lewis acid is a metal atom or ion, especially but not necessarily one drawn from the d-block of the periodic table (a ‘transition metal’). The d-block consists of the elements that make up the skinny central rectangle of the periodic table. They include important constructional metals, such as iron, nickel, and copper, and also the chemically aloof ‘noble’ metals gold, platinum, and silver. The Lewis base that I focus on will be a molecule or ion that also has an independent existence in the wild, such as water, H2O, or ammonia, NH3. In most cases the complex consists of the central metal atom or ion with up to six Lewis bases clustering around it. In this context, the Lewis bases are known as ‘ligands’ (from the Latin for ‘bound’) and I shall use that term here. I don’t want you to think that I am embarking on stratospherically esoteric material again. These metal complexes are hugely important in many aspects of the everyday world. For instance, chlorophyll is a complex of magnesium and is responsible for capturing the energy of the Sun for photosynthesis (Reaction 26). There is hardly a more important molecule. One that comes close in importance is haemoglobin, an elaborate complex of iron, which ensures that oxygen reaches all your cells and keeps you alive. Many pigments are complexes, so your life is decorated and made more colourful by them. Some pharmaceuticals are complexes based on platinum, so one day, perhaps even now, you might be kept alive by one of these artificial complexes.

On the generation of oxirene and dimethyloxirene by retro-Diels–Alder reactions, and reactions of dimethyloxirene: a computational study

2002 ◽  
Vol 80 (1) ◽  
pp. 94-105 ◽  
Author(s):  
C Delamere ◽  
C Jakins ◽  
E Lewars
Keyword(s):  
Transition State ◽  
Ring Opening ◽  
Computational Study ◽  
Single Point ◽  
Diels Alder ◽  
Reaction Energy ◽  
One Step ◽  
Reaction Energies ◽  
Level 1 ◽  
Late Transition

The isomerization of oxirene (oxacyclopropene) (1) to ketene, dimethyloxirene (7) to dimethylketene via the oxo carbene ("ketocarbene"), and the retro-Diels–Alder extrusion of oxirene and dimethyloxirene from their formal adducts (9 and 24, respectively) with benzene were studied computationally. All species were optimized at the MP2(fc)/6–31G(df,p) level; the species involving 1 were also subjected to MP2(fc)/6–31G(df,p) frequency and single-point CCSD(T)/6–31G(df,p) calculations. At the CCSD(T)/6–31G(df,p)//MP2(fc)/6–31G(df,p) level 1 isomerized to ketene in one step with a barrier of 2.8 kJ mol–1 and a reaction energy of –320.6 kJ mol–1. The extrusion of 1 from 9 had a late transition state and activation and reaction energies of 264.2 and 214.2 kJ mol–1, respectively, cf. cyclopropene extrusion from its adduct (192.3 and 95.9 kJ mol–1), indicating an antiaromatic destabilization energy of 214.2 – 95.9 = 118 kJ mol–1 for 1. The carbene 8 from ring-opening of 7 lay 10.9 kJ mol–1 above 7 (CCSD(T)/6–31G(df,p)//MP2(fc)/6–31G(df,p)), but the transition state could not be found; 8 isomerized to dimethylketene (252.7 kJ mol–1 below 7) with a barrier of 16.4 kJ mol–1, and to s-(Z)- and s-(E)-butenone with barriers of 28.5 and 35.4 kJ mol–1, respectively. The UV (TDDFT, B3P86/6–311++G**//MP2(fc)/6–31G(df,p)) spectra of 1 and 7 were calculated. Discrepancies were seen between the calculated IR spectra of 7 (bis(trifluoromethyl)oxirene) and perfluoro ethyl methyloxirene, and those attributed to these species in earlier matrix-isolation work. Key words: oxirene, dimethyloxirene, ab initio, retro-Diels–Alder, Diels–Alder.

Amino and cyano N atoms in competitive situations: which is the best hydrogen-bond acceptor? A crystallographic database investigation

2001 ◽  
Vol 57 (6) ◽  
pp. 850-858 ◽  
Author(s):  
Nahossé Ziao ◽  
Jérôme Graton ◽  
Christian Laurence ◽  
Jean-Yves Le Questel
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Amino Nitrogen ◽  
Lone Pair ◽  
Molecular Surface ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Acceptor

The relative hydrogen-bond acceptor abilities of amino and cyano N atoms have been investigated using data retrieved from the Cambridge Structural Database and via ab initio molecular orbital calculations. Surveys of the CSD for hydrogen bonds between HX (X = N, O) donors, N—T—C≡N (push–pull nitriles) and N—(Csp 3) n —C≡N molecular fragments  show that the hydrogen bonds are more abundant on the nitrile than on the amino nitrogen. In the push–pull family, in which T is a transmitter of resonance effects, the hydrogen-bonding ability of the cyano nitrogen is increased by conjugative interactions between the lone pair of the amino substituent and the C≡N group: a clear example of resonance-assisted hydrogen bonding. The strength of the hydrogen-bonds on the cyano nitrogen in this family follows the experimental order of hydrogen-bond basicity, as observed in solution through the pK HB scale. The number of hydrogen bonds established on the amino nitrogen is greater for aliphatic aminonitriles N—(Csp 3) n —C≡N, but remains low. This behaviour reflects the greater sensitivity of the amino nitrogen to steric hindrance and the electron-withdrawing inductive effect compared with the cyano nitrogen. Ab initio molecular orbital calculations (B3LYP/6-31+G** level) of electrostatic potentials on the molecular surface around each nitrogen confirm the experimental observations.

Computed thermodynamic stabilities of silylium Lewis base adducts

2018 ◽  
Vol 16 (13) ◽  
pp. 2318-2323 ◽  
Author(s):  
Christina A. Roselli ◽  
Michel R. Gagné
Keyword(s):  
Computational Study ◽  
Lewis Base ◽  
Lewis Bases

We report a computational study of the transfer of silylium from phosphine to heteroatom containing Lewis bases including ethers, phosphines, and amines.

Ab initio MO Calculations on the Structure and Raman and Infrared Spectra of [Al4O2Cl10]2– Oxide in Chloroaluminate Melts

2007 ◽  
Vol 62 (3-4) ◽  
pp. 157-168
Author(s):  
Rolf W. Berg
Keyword(s):  
Ab Initio ◽  
Vibrational Analysis ◽  
Binding Energies ◽  
Aluminium Chloride ◽  
Molecular Orbital Calculations ◽  
Oxide Content ◽  
Ir Absorption ◽  
Convergence Criteria ◽  
Model Calculations ◽  
Bonding System

The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures may be formed in addition to [AlCl4]−: [Al2OCl6]2−, [Al3OCl8]−, [Al2O2Cl4]2−, [Al3O2Cl6]− and [Al4O2Cl10]2−. Ab initio molecular orbital calculations are carried out on these various aluminium chloride and oxochloride ions, in assumed isolated gaseous free ionic state, by use of the Gaussian 03W program at the restricted Hartree-Fock (HF) level and with the 6-31+G(d,p) basis set.Without any pre-assumed symmetries and with tight optimization convergence criteria and by using the modified GDIIS algorithm, the model calculations generally converge. The structures and their binding energies are presented. The expected geometries are supported, with one exception perhaps being the [Al2OCl6]2− ion, that gave a linear Al-O-Al bonding system of staggered AlCl3-groups (approximate D3d symmetry), in analogy to the linear Al-O-Al geometry of the analogous [Al2OF6]2− ion, found previously. The calculations include determination of the vibrational harmonic normal modes and the infrared and Raman spectra (vibrational band wavenumbers and intensities), without any empiric adjustments of the harmonic force constants, using constants directly predicted from the Gaussian 03W program. Previously obtained IR absorption and Raman scattering spectra of melts are assigned, by comparing to the ab initio quantum mechanical vibrational analysis results. It is concluded that the small oxide content commonly found in basic and neutral tetrachloroaluminate melts, most probably consists of [Al4O2Cl10]2− ions, and the vibrational spectra are given.

Hydrogen-Bond Acceptor Properties of Nitro-O Atoms: A Combined Crystallographic Database and Ab Initio Molecular Orbital Study

1997 ◽  
Vol 53 (6) ◽  
pp. 1017-1024 ◽  
Author(s):  
F. H. Allen ◽  
C. A. Baalham ◽  
J. P. M. Lommerse ◽  
P. R. Raithby ◽  
E. Sparr
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Molecular Orbital ◽  
Lone Pair ◽  
Basis Set ◽  
Molecular Orbital Calculations ◽  
Hydrogen Bond Energy ◽  
Hydrogen Bond Acceptor ◽  
Model Dimer

Crystallographic data for 620 C—nitro-O...H—N,O hydrogen bonds, involving 560 unique H atoms, have been investigated to the van der Waals limit of 2.62 Å. The overall mean nitro-O...H bond length is 2.30 (1) Å, which is much longer (weaker) than comparable hydrogen bonds involving >C=O acceptors in ketones, carboxylic acids and amides. The donor hydrogen prefers to approach the nitro-O atoms in the C—NO2 plane and there is an approximate 3:2 preference for hydrogen approach between the two nitro-O atoms, rather than between the C and O substituents. However, hydrogen approach between the two O acceptors is usually strongly asymmetric, the H atom being more closely associated with one of the O atoms: only 60 H atoms have both O...H distances \leq 2.62 Å. The approach of hydrogen along putative O-atom lone-pair directions is clearly observed. Ab-initio-based molecular orbital calculations (6-31G** basis set level), using intermolecular perturbation theory (IMPT) applied to the nitromethane–methanol model dimer, agree with the experimental observations. IMPT calculations yield an attractive hydrogen-bond energy of ca −15 kJ mol−1, about half as strong as the >C=O...H bonds noted above.

In Silico Docking, ADMET and QSAR Study of few Antimalarial Phytoconstituents as Inhibitors of Plasmepsin II of P. falciparum Against Malaria

2020 ◽  
Vol 15 (3) ◽  
pp. 264-273
Author(s):  
Syeda Sabiha Salam ◽  
Pankaj Chetia ◽  
Devid Kardong
Keyword(s):  
Medicinal Plants ◽  
In Silico ◽  
Computational Study ◽  
Binding Energies ◽  
Eastern Region ◽  
Relationship Analysis ◽  
The North ◽  
North Eastern ◽  
Plasmepsin Ii ◽  
Antimalarial Compounds

Background: Malaria is endemic in various parts of India particularly in the North- Eastern states with Plasmodium falciparum-the most prevalent human malaria parasite. Plantderived compounds have always received tremendous importance in the area of drug discovery and development and scientific study of traditional medicinal plants are of great importance to mankind. Objective: The present work deals with the computational study of some antimalarial compounds obtained from a few medicinal plants used by the tribal inhabitants of the North-Eastern region of India for treating malaria. Methods: In silico methodologies were performed to study the ligand-receptor interactions. Target was identified based on the pharmacophore mapping approach. A total of 18 plant-derived compounds were investigated in order to estimate the binding energies of the compounds with their drug target through molecular docking using Autodock 4.2. ADMET filtering for determining the pharmacokinetic properties of the compounds was done using Mobyle@RPBS server. Subsequent Quantitative-Structure Activity Relationship analysis for bioactivity prediction (IC50) of the compounds was done using Easy QSAR 1.0. Results: The docking result identified Salannin to be the most potent Plasmepsin II inhibitor while the QSAR analysis identified Lupeol to have the least IC50 value. Most of the compounds have passed the ADME/Tox filtration. Conclusion: Salannin and Lupeol were found to be the most potent antimalarial compounds that can act as successful inhibitors against Plasmepsin II of P. falciparum. The compounds Salannin and Lupeol are found in Azadirachta indica and Swertia chirata plants respectively, abundantly available in the North-Eastern region of India and used by many inhabiting tribes for the treatment of malaria and its symptoms.

scholarly journals Relativistic Effects on NMR Parameters of Halogen-Bonded Complexes

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4399 ◽  
Author(s):  
Ibon Alkorta ◽  
José Elguero ◽  
Manuel Yáñez ◽  
Otilia Mó ◽  
M. Merced Montero-Campillo
Keyword(s):  
Relativistic Effects ◽  
Lewis Base ◽  
Coupling Constants ◽  
Basic Site ◽  
Lewis Bases ◽  
Nmr Parameters ◽  
Quadrupolar Coupling ◽  
Binary Complexes ◽  
Computational Level ◽  
Bonded Complexes

Relativistic effects are found to be important for the estimation of NMR parameters in halogen-bonded complexes, mainly when they involve the heavier elements, iodine and astatine. A detailed study of 60 binary complexes formed between dihalogen molecules (XY with X, Y = F, Cl, Br, I and At) and four Lewis bases (NH3, H2O, PH3 and SH2) was carried out at the MP2/aug-cc-pVTZ/aug-cc-pVTZ-PP computational level to show the extent of these effects. The NMR parameters (shielding and nuclear quadrupolar coupling constants) were computed using the relativistic Hamiltonian ZORA and compared to the values obtained with a non-relativistic Hamiltonian. The results show a mixture of the importance of the relativistic corrections as both the size of the halogen atom and the proximity of this atom to the basic site of the Lewis base increase.

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