Research Highlights
Theoretical Study of the Molecular Aspect of the Suspected Novichok Agent A234 of the Skripal Poisoning
H. Bhakhoa, L. Rhyman and P. Ramasami
Novichoks are the suspected nerve agents in the March 2018 Skripal poisoning. In this context, the novichok agent A234 (chemical structure proposed by Mirzayanov) was studied using computational methods to shed light on its molecular, electronic, spectroscopic, thermodynamic and toxicity parameters as well as on potential thermal and hydrolysis degradation pathways. The poisoning action and antidote of A234 were also investigated. Some of these parameters were compared to three common G- and V-series nerve agents, namely GB, VR and VX. The research findings should be useful towards the detection, development of antidotes and destruction of A234.
Synthesis, Characterization, DFT and Antimicrobial Studies of Transition Metal Ion Complexes of a New Schiff Base Ligand, 5-Methylpyrazole-3yl-N-(2́-hydroxyphenylamine)methyleneimine, (MPzOAP)
S. Mandal, M. Das, P. Das, A. Samanta, R. J. Butcher, M. Saha, I. A. Alswaidan, L. Rhyman, P. Ramasami and N. C. Saha
A new pyrazole containing Schiff base ligand and its Co(III), Ni(II), Cu(II), Zn(II), Cd(II) and Hg(II) complexes have been synthesized & characterized. The reported NNO tridentate ligand (MPzOAP) binds with the metal ion via the tertiary nitrogen atom of pyrazole ring, the azomethine nitrogen and the phenolic oxygen atom. The structural conformation of the ligand has been established by X-ray study. The structures of the ligand and the metal ion complexes are also investigated using the DFT method. The In vitro antimicrobial activities of the ligand and the complexes have been reported and the mode of action against some pathogenic bacteria, studied by scanning electron microscopy (SEM), is shown.
Ingenious Bioorganic Adsorbents For The Removal Of Distillery Based Pigment- Melanoidin: Preparation and Adsorption Mechanism
S. Vivekanandam, V. Muthunarayanan, S. Muniraj, L. Rhyman, I. A. Alswaidan and P. Ramasami,
Journal of Macromolecular Science, Part A: Pure and Applied Chemistry, 2019, 56, 52-62
Melanoidins are composite biopolymers which consist of amino carbonyl compounds which are the major coloring and polluting elements of distillery effluent. In this study, a synthetic melanoidin was used as a model for natural melanoidins, the chief colorant of the effluent. Deportations of melanoidins were investigated using both natural adsorbents and constructed microbial consortia based adsorbents and denoting it using the adsorption isotherms and SEM analysis. A review enabled us to assess about the valuation of the prepared low cost adsorbent and microbial coated adsorbents and for the treatment of the synthetic melanoidin solution. Based on the performances, both Microbial Coated Commercially Activated Carbon (MCCAC) and Commercially Activated Carbon (CAC) were better when compared with the other adsorbents at lower melanoidin concentrations; however, at higher melanoidin concentration, MCCAC performed better. The utilization of CAC for the removal of melanoidins may be cost competitive; hence Microbial Coated Procured Prosopsis Activated Carbon (MCPPAC) can be used as a substitute for the removal systems. Therefore, the microbial coated adsorbents can be a remedy for the removal of color through expatriation of melanoidin from the distillery effluents.
Synthesis, Spectroscopic, Biological and DFT Studies of New t-Butyl Substituted Salicylaldimines having Disulfide Moiety
M. G. Bhowon, S. Jhaumeer Laulloo, E. C. Hosten, M. M. Khodabaccus, L. Rhyman and P. Ramasami
In this study, two new t-butyl substituted salicyladimines, N,N′-bis(5-t-butylsalicylidene) diphenyl disulphide-2,2′-diamine and N,N′-bis(3-t-butylsalicylidene) diphenyl disulphide-2,2′-diamine were synthesized and characterized by spectroscopy and X-ray diffractometry. The effect of the t-butyl group on the keto-enol tautomerism in solution and solid state was investigated. According to X-ray and spectroscopic data (UV–Vis), both salicyladimines were found to be mainly in the enol-tautomeric form. Density functional theory (DFT) method was used to complement this research work. The theoretical results are in good agreement with those obtained experimentally. The anti-oxidant and anti-bacterial activities of the substituted salicyladimines were compared to the parent Schiff base, N,N′-bis(salicylidene) diphenyl disulphide-2,2′-diamine. The t-butyl derivatives show enhanced activity which can be related to the enol form of the Schiff bases and possibly due to the increase in dipole and quadrupole moments in addition to increase in hydrophobicity and decrease solubility in water.
Theoretical Investigation of Difluoroboron Complex of Curcuminoid Derivatives with and without Phenyl Substituent (at Meso Position): Linear and Non‐Linear Optical Study
M. M. Raikwar, L. Rhyman, P. Ramasami and N. Sekar
Two difluoroboron curcumin analogs and their phenylated versions were studied for their photophysical and non‐linear optical properties based on comprehensive density functional theory approach. The ground state geometry optimization, vertical excitation, and the first excited state optimization were carried out using B3LYP and CAM−B3LYP functionals with 6–31G(d) basis set. The geometry of the difluoroboron curcumin analogs was found to remain planar in both the ground and excited states. The computed vertical excitation and emission values obtained with global hybrid functional are in good correlation with the observed values. The phenylated analogs show enhancement in the photophysical properties. The linear and non‐linear optical properties were computed using two global hybrids functionals (B3LYP and BHHLYP) and a range separated hybrid functional (CAM−B3LYP) with 6–31+G(d,p) basis set. The difluoroboron curcumin analogs without the phenyl substituent have larger polarizability and hyperpolarizabiliy parameters than the phenylated analogs. The polarizability and hyperpolarizabiliy were found to be comparable with the BHHLYP and CAM−B3LYP functionals.
ExcelAutomat 1.3: Fragment Analysis based on the Distortion/Interaction-Activation Strain Model
J. Z. A. Laloo, N. Savoo, N. Laloo, L. Rhyman and P. Ramasami
The distortion/interaction‐activation strain model (D/I‐ASM), a fragment analysis method, is applied to study the structure–reactivity relationship in reactions. The application of D/I‐ASM involves the generation of input files for points along a reaction profile, submission of input files to a quantum software package, processing of parameters from the resulting output files and generation of graphical plots. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667) provides a framework and library in Visual Basic for Application programming language to process such files. New routines were written in ExcelAutomat 1.3 to facilitate processing of files for D/I‐ASM. The worksheet “ASM” was included where initial parameters needed can be defined. The routines for D/I‐ASM were tested successfully on bimolecular nucleophilic substitution, cycloaddition, and barrierless reactions. The automation of fragment analysis by ExcelAutomat 1.3 is compatible with Microsoft Excel and LibreOffice Calc. The extensible tool processes files from Gaussian and GAMESS‐US packages.
DFT Exploration of [3+2] Cycloaddition Reaction of 1H-Phosphorinium-3-olate and 1-Methylphosphorinium-3-olate with Methyl Methacrylate
D. Hallooman, M. Ríos-Gutiérrez, L. Rhyman, I. A. Alswaidan, L. R. Domingo and P. Ramasami
A Molecular Electron Density Theory (MEDT) study of the regio- and stereoselectivity of the [3 + 2] cycloaddition (32CA) reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl methacrylate was carried out using the B3LYP/6-31G(d) method. In order to test the method dependence for the most favorable reaction path leading to the 1H-substituted 6-exo cycloadduct (CA) various functionals using higher basis sets were taken into consideration in the gas phase. An analysis of the energetic parameters indicates that the reaction paths leading to 6-exo CA are kinetically as well as thermodynamically favored in the gas phase, THF and ethanol. The calculated energetic parameters of the 32CA reactions of these phosphorus derivatives were compared with those of methyl acrylate and their nitrogen analogues. Investigation of the global electron density transfer at the TSs indicates that these 32CA reactions have non-polar character, while ELF topological analysis of the C–C bond formation along the most favorable reaction path indicates that these 32CA reactions take place through a non-concerted two-stage one-step mechanism, via highly asynchronous TSs.
Effect of Methoxy Group on NLOphoric Properties of Fluorescent 7-arylstyryl-2-methoxyphenylimidazo [1, 2-a] pyridine-Solvatochromic and Computational Method
S. D. Jadhav, I. A. Alswaidan, L. Rhyman, P. Ramasami and N. Sekar
Extensively conjugated donor-π-acceptor-donor (D-π-A-π-D) type fluorescent styryl dyes bearing imidazo[1,2-a]pyridine units have been investigated for their nonlinear optical properties (NLO). Enhanced Stokes shift (2486–2843 cm−1) brought about by replacing methoxy group by diethyl, dimethyl, cyclohexylamino substituents at C-2 and C-7 positions of imidazo[1,2-a]pyridine core in styryl dyes have been understood in elucidating the electronic structures. The position of methoxy group acting as auxiliary donor largely influences the nonlinear optical (NLO) properties of imidazo[1,2-a]pyridine derivatives. Polarizabilities and hyperpolarizabilies were estimated by solvatochromic and DFT method using BHandHLYP and CAM-B3LYP functionals with the 6-311 + G(d,p) basis set. Imidazo[1,2-a]pyridine derivatives showed minimum ten-fold higher NLO parameters compared to reminiscent of charge transfer contribution of donor groups. The dyes have two-photon cross-section values 66–189 GM and comparable with commercial two photon absorbing styryl dyes.
Spectroscopic and DFT Approach for Structure Property Relationship of Red Emitting Rhodamine analogues: A Study of Linear and Nonlinear Optical Properties
A. G. Jadhav, L. Rhyman, I. A. Alswaidan, P. Ramasami and N. Sekar
Linear and nonlinear optical (NLO) properties of triphenyl fused rhodamine analogues were estimated by spectroscopic based mathematical calculations and compared with computed values using density functional theory (DFT) calculations. Various Global hybrids (GHs) and range separated hybrids (RSHs) were utilized for reliable estimations of NLO properties. Spectroscopic based mathematical calculations of polarizability (αCT), first order hyperpolarizability (βCT) and second order hyperpolarizability (γ) were performed in varying polarity solvents. Spectroscopic based mathematical calculted αCT, βCT and γ values are found to have much closer agreement with the DFT computed values obtained by using RSHs. Comparative analysis of αCT, βCT and γ values suggested that these values increases with the increase of triphenylamine substitutions. Moreover, αCT, βCT and γ values increase with decreasing HOMO-LUMO band gap for all the dyes. N-[9-(isobenzofuran-1(3H)-one)-6-(dipnenylamino)-xanthene]-N-diphenyl amine having bis-triphenylamine substituent showed the largest NLO response among all analogues dyes.
Photoelectrocatalytic Application of Palladium Decorated Zinc Oxide-Expanded Graphite Electrode for the Removal of 4-Nitrophenol: Experimental and Computational Study
E. H. Umukoro, M. G. Peleyeju, A. O. Idris, J. C. Ngila, N. Mabuba, L. Rhyman, P. Ramasami and O. A. Arotiba
A novel Pd–ZnO-expanded graphite (EG) photoelectrode was constructed from a Pd–ZnO-EG nanocomposite synthesised by a hydrothermal method and characterised using various techniques such as X-ray diffractometry (XRD), Raman spectroscopy, UV-Vis diffuse reflectance spectroscopy, nitrogen adsorption–desorption analysis, transmission electron microscopy (TEM), scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS). Cyclic voltammetry and photocurrent response measurements were also carried out on the electrode. The Pd–ZnO-EG electrode was employed in the photoelectrocatalytic removal of 4-nitrophenol as a target water pollutant at a neutral pH and with a current density of 7 mA cm−2. Optical studies revealed that the Pd–ZnO-EG absorbed strongly in the visible light region. The Pd–ZnO-EG electrode showed improved photoelectrocatalytic activity in relation to ZnO-EG and EG electrodes for the removal of the 4-nitrophenol. The photocurrent responses showed that the Pd–ZnO-EG nanocomposite electrode could be employed as a good photoelectrode for photoelectrocatalytic processes and environmental remediation such as treatment of industrial waste waters. Density functional theory method was used to model the oxidative degradation of 4-nitrophenol by the hydroxyl radical which generates hydroquinone, benzoquinone, 4-nitrocatechol, 4-nitroresorcinol and the opening of the 4-nitrophenol ring. Furthermore, the hydroxyl radical is regenerated and can further oxidise the ring structure and initiate a new degradation process.
Ion-Pair SN2 Reaction of OH- and CH3Cl: Activation Strain analyses of Counterion and Solvent Effects
J. Z. A. Laloo, L. Rhyman, O. Larrañaga, P. Ramasami, F. M. Bickelhaupt and A. de Cozar
We have theoretically studied the non‐identity SN2 reactions of MnOH(n−1)+CH3Cl (M+=Li+, Na+, K+, and MgCl+; n=0, 1) in the gas phase and in THF solution at the OLYP/6‐31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M+ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (SN2‐b) and frontside (SN2‐f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.
Synthesis, Characterization, Anti-microbial Screening and Computational Studies ofa Tripodal Schiff Base containing Pyrimidine Unit
U. S. Oruma, P. O. Ukoha, L. Rhyman, M. I. Elzagheid, L. N. Obasi, P. Ramasami and K. Jurkschat
A novel tripodal Schiff base ligand, 5‐amino‐2,4,6‐tris(4‐carboxybenzimino)‐1,3‐pyrimidine (TTPS), was synthesized for the first time by the reaction of 2,4,5,6‐tetraaminopyrimidine with 4‐carboxybenzaldehyde. The ligand was characterized by means of ultraviolet–visible, Fourier transform infrared, one‐dimensional 1H‐NMR, and one‐dimensional 13C‐NMR spectroscopies and elemental microanalysis. The Fourier transform infrared and NMR studies revealed that one of the NH2 group in 2,4,5,6‐tetraaminopyrimidine is not involved in bonding. The in vitro antimicrobial activities of the ligand were investigated against Gram‐negative bacteria: Escherichia coli (ATCC 6749) and Pseudomonas aeruginosa (ATCC 9027), Gram‐positive bacteria: Staphylococcus aureus (ATCC 6538P) and Bacillus cereus (ATCC 14579), and fungi: Candida albicans and Aspergillus niger by the agar well diffusion technique. TTPS exhibits good activity against the test microorganisms. The minimum inhibitory concentrations of TTPS against S. aureus were compared with tetracycline and gentamicin, which are conventional bacterial drugs. The upper level of Lorke's method was used to determine the acute toxicity of the compound. The acute toxicity test indicates that TTPS is toxic at doses above 2154 mg/kg. The in vivo antimalarial assay was carried out on Plasmodium berghei based on the 4‐day suppressive method. The result shows a general dose‐dependent significant parasitemia inhibition compared with the negative control with TTPS having inhibition of 72.20% at 50 mg/kg and 65.81% at 25 mg/kg close to the value (87.22%) of the standard drug artesunate 5 mg/kg. Density functional theory method was used to complement this experimental investigation.
Novel Coumarin Rhenium(I) and -(V) Complexes: Formation, DFT and DNA Binding Studies
B. Jadoo, I. N. Booysen, M. P. Akerman, L. Rhyman and P. Ramasami
Herein, we report the formation and characterisation of novel rhenium(I) and -(V) compounds with coumarin bidentate chelates: trans-[ReOBr2(PPh3)(hbc)] (1) (Hhbc = 7-(2-hydroxybenzylideneamino)-4-(trifluoromethyl)-2H-chromen-2-one), fac-[Re(CO)3Cl(aomc)] (2) (aomc = 7-(((2-amino-4-oxo-4H-chromen-3-yl)methylene)amino)-4-(trifluoromethyl)-2H-chromen-2-one) and fac-[Re(CO)3Cl(moac)] (3) (moac = 7-(((2-methoxy-4-oxochroman-3-yl)methylene)amino)-4-(trifluoromethyl)-2H-chromen-2-one). The coumarin free-ligands and the metal complexes 1–3 were characterized by NMR, UV–Vis and FTIR spectroscopy, melting point and molar conductivity measurements as well as time-of-flight mass spectrometry. Their structural elucidations were supported by the respective solid state structures of 1, Hhbc and moac. DNA binding studies conducted using the facial tricarbonylrhenium(I) complexes 2 and 3, revealed that they are DNA groove binders with intrinsic binding constants in the order of 105 and 104 M bp, respectively. This study was also complemented using density functional theory (DFT) and time-dependent DFT methods to attain a deeper understanding into the structural parameters, infrared and electronic spectra of these coumarin free-ligands and their metal complexes 1–3.
Excited State and Non-linear Optical Properties of NIR Absorbing β-Thiophene-Fused BF2-Azadipyrromethene Dyes—Computational Investigation
Y. Gawale, L. Rhyman, M. I. Elzagheid, P. Ramasami and N. Sekar
Density functional theory and time-dependent density functional theory computations were used to understand the electronic and photophysical parameters of NIR β-thiophene-fused BF2-azadipyrromethene dyes. The computed data are in good agreement with those obtained experimentally and they provide insights into the origin of red shifted optical spectra compared to the parent aza-BODIPY, low Stokes shift, non-linear optical responses and quantitative description of the singlet–triplet energy gap. The resultant decrease in the HOMO − LUMO energy gap is responsible for the red shift. The possible use as non-linear optical materials is supported by large enhancement in the non-linear optical properties. On the basis of vertical triplet energies, their possible potential therapeutic use as a photosensitizer in photodynamic therapy is proposed. The singlet–triplet energetic gaps suggest that the β-thiophene-fused BF2-azadipyrromethene dyes can act as a sensitizer to produce an efficient generation of singlet oxygen. Their optimal use as an efficient singlet fission materials has been proposed on the basis of excitation energies in the ground, lowest singlet and triplet excited states.
Synthesis, Characterization and Computational Studies of
3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol and Molecular Structure of its Zwitterionic Form
J. C. Ezeorah, V. Ossai, L. N. Obasi, M. I. Elzagheid, L. Rhyman, M. Lutter, K. Jurkschat,
N. Dege and P. Ramasami
The Schiff base 3-{(E)-[(2-hydroxyphenyl)imino]methyl}benzene-1,2-diol was synthesized by the condensation of 2,3-dihydroxybenzaldehyde and 2-aminophenol in water at room temperature. The crystal was grown using two solvents (dry methanol and 60% methanol). The compound was characterized using elemental microanalysis, IR, NMR, UV spectroscopies and single-crystal X-ray diffraction crystallography. The X-ray structure reveals that the Schiff base crystallizes as a methanol solvate in dry methanol with triclinic crystal system, space group P-1 and Z = 2 in the unit cell and as a non-methanol solvate in 60% methanol with triclinic crystal system, space group P-1 and Z = 4 in the unit cell. The compound showed absorption bands at 272, 389, 473 and 602 nm in DMSO. These bands were assigned as π → π∗, n → π∗ and n-σ∗ transitions. The 473 and 602 nm bands in DMSO reveal that the compound exists in tautomeric forms. The presence of N-H, C-O and C=N stretching vibrations in the IR spectrum indicates that the compound is zwitterionic in the solid state. This study was supplemented using density functional theory method.
Understanding the Intramolecular Diels-Alder Reactions of N-Substituted N-Allyl-Furfurylamines: An MEDT Study
D. Hallooman, M. Ríos-Gutiérrez, L. Rhyman, I. A. Alswaidan, M. I. Elzagheid, L. R. Domingo and P. Ramasami
ChemistrySelect, 2017, 2, 9736-9743
The intramolecular Diels-Alder (IMDA) reactions of N-allylfurfurylamine (1a) and N-trityl-allyl-furfurylamine (1b), were studied within the molecular electron density theory (MEDT) using density functional theory method [B3LYP/6-31G(d)]. In spite of the high activation enthalpies, the low unfavourable activation entropies associated to these intramolecular processes permits these IMDA reactions to take place. The IMDA reaction of 1a is thermodynamically unfavourable. The presence of the bulky -CPh3 group in the amine nitrogen atom that destabilises the extended conformation of 1b turns the process into an exergonic one. This behaviour does not only affect the thermochemistry of the reaction, but also the kinetic parameters, thus accelerating the reaction. Electron localization function topological analysis of the C-C single bond formation along the IMDA reaction of 1a shows a bonding pattern similar to non-polar intermolecular Diels-Alder reactions. The present MEDT study explains the experimental results; although the steric buttress is able to change the direction of these reversible IMDA reactions.
A Study of the Group 1 Metal Tetra-aza Macrocyclic Complexes
[M(Me4cyclen)(L)]+ using Electronic Structure Calculations
H. Bhakhoa, L. Rhyman, E. P. Lee, D. K. W. Mok, P. Ramasami and J. M. Dyke
Dalton Transations, 2017, 46, 15301-15310
Metal-cyclen complexes have a number of important applications. However, the coordination chemistry between metal ions and cyclen-based macrocycles is much less well studied compared to their metal ion-crown ether analogues. This work, which makes a contribution to address this imbalance by studying complex ions of the type [M(Me4cyclen)(L)]+, was initiated by results of an experimental study which prepared some Group 1 metal cyclen complexes, namely [Li(Me4cyclen)(H2O)][BArF] and [Na(Me4cyclen)(THF)][BArF] and obtained their X-ray crystal structures [J. M. Dyke, W. Levason, M. E. Light, D. Pugh, G. Reid, H. Bhakhoa, P. Ramasami, and L. Rhyman, Dalton Trans., 2015, 44, 13853]. The lowest [M(Me4cyclen)(L)]+ minimum energy structures (M = Li, Na, K, and L = H2O, THF, DEE, MeOH, DCM) are studied using density functional theory (DFT) calculations. The geometry of each [M(Me4cyclen)(L)]+ structure and, in particular, the conformation of L are found to be mainly governed by steric hindrance which decreases as the size of the ionic radius increases from Li+ → Na+ → K+. Good agreement of computed geometrical parameters of [Li(Me4cyclen)(H2O)]+ and [Na(Me4cyclen)(THF)]+ with the corresponding geometrical parameters derived from the crystal structures [Li(Me4cyclen)(H2O)]+[BArF]– and [Na(Me4cyclen)(H2O)]+[BArF]– is obtained. Bonding analysis indicates that the stability of the [M(Me4cyclen)(L)]+ structures originates mainly from ionic interaction between the Me4cyclen/L ligands and the M+ centres. The experimental observation that [M(Me4cyclen)(L)]+[BArF]– complexes could be prepared in crystalline form for M+ = Li+ and Na+, but that experiments aimed at synthesising the corresponding K+, Rb+, and Cs+ complexes failed resulting in formation of [Me4cyclenH][BArF] is investigated using DFT and explicitly correlated calculations, and explained by considering production of [Me4cyclenH]+ by a hydrolysis reaction, involving traces of water, which competes with [M(Me4cyclen)(L)]+ formation. [Me4cyclenH]+ formation dominates for M+ = K+, Rb+, and Cs+ whereas formation of [M(Me4cyclen)(L)]+ is energetically favoured for M+ = Li+ and Na+. The results indicate that the number and type of ligands, play a key role in stabilising the [M(Me4cyclen)+ complexes and it is hoped that this work will encourage experimentalists to prepare and characterise other [M(Me4cyclen)(L)]+ complexes.
Molecular, Vibrational and Electronic Structure of 4-Bromo-2-halogenobenzaldehydes: Halogen and Solvent Effect
D. Fernández, C. Parlak, M. Bilge, M. F. Kaya, M. Tursun, G. Keşan, L. Rhyman,
P. Ramasami and M. Şenyel
Physical Sciences Reviews, 2017, 2, 58
The halogen and solvent effects on the structure of 4-bromo-2-halogenobenzaldehydes [C7H4BrXO; X = F (BFB), Cl (BCB) or Br (BBB)] were investigated by the density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The B3LYP functional and HF and MP2 levels of theory were used with the 6-311+G(3df,p) or aug-cc-pVDZ basis sets. Computations were focused on the cis and trans conformers of the investigated compounds in the gas phase and solutions of 18 different polar or non-polar organic solvents. The computed frequencies of the C=O stretching vibration of the compounds were correlated with some empirical solvent parameters such as the Kirkwood–Bauer–Magat (KBM) equation, solvent acceptor number (AN), Swain parameters and linear solvation energy relationships (LSERs). The electronic properties of the compounds were also examined. The present work explores the effects of the medium and halogen on the conformation, geometrical parameters, dipole moment, ν(C=O) vibration, UV data, frontier orbitals and density-of-states diagram of the compounds. The findings of this research can be useful for studies on benzaldehydes.
Triphenylamine-based fluorescent NLO phores with ICT characteristics: Solvatochromic and Theoretical study
S. B. Katariya, D. Patil, L. Rhyman, I. A. Alswaidan, P. Ramasami and N. Sekar
Journal of Molecular Structure, 2017, 1150, 493-506
The static first and second hyperpolarizability and their related properties were calculated for triphenylamine-based “push-pull” dyes using the B3LYP, CAM-B3LYP and BHHLYP functionals in conjunction with the 6-311+G(d,p) basis set. The electronic coupling for the electron transfer reaction of the dyes were calculated with the generalized Mulliken-Hush method. The results obtained were correlated with the polarizability parameter αCT, first hyperpolarizability parameter βCT, and the solvatochromic descriptor of 〈γ〉SD obtained by the solvatochromic method. The dyes studied show a high total first order hyperpolarizability (70–238 times) and second order hyperpolarizability (412–778 times) compared to urea. Among the three functionals, the CAM-B3LYP and BHHLYP functionals show hyperpolarizability values closer to experimental values. Experimental absorption and emission wavelengths measured for all the synthesized dyes are in good agreement with those predicted using the time-dependent density functional theory. The theoretical examination on non-linear optical properties was performed on the key parameters of polarizability and hyperpolarizability. A remarkable increase in non-linear optical response is observed on insertion of benzothiazole unit compared to benzimidazole unit.
Synthesis, Characterization, Antimicrobial Screening and in silico Studies of Schiff Bases Derived from Trans-para-methoxycinnamaldehyde
N. L. Obasi, G. U. Kaior, A. Ibezim, A. E. Ochonogor, L. Rhyman, V. Uahengo, M. Lutter,
K. Jurkschat and P. Ramasami
Journal of Molecular Structure, 2017, 1149, 8-16
Two Schiff bases namely N,N′-Bis-[3-(4-metoxy-phenyl)-allylidene]ethane-1,2-diamine (TPMC/EDA) and [3-(4-methoxy-phenyl)-allylidene]-phenyl-amine (TPMC/AN) were synthesized. They were characterized using elemental microanalysis, IR, NMR, UV and mass spectroscopies. Single crystals of TPMC/AN were also analyzed by X-ray diffraction and the compound was examined using B3LYP/6–311++G(d,p) method. A Monoclinic crystal system and space groups of P21/c were obtained for the crystal. Docking calculations on the compounds showed they interacted with fungal N-myristoyltransferase and bacteria DNA gyrase at 2.62–2.95 and 190.26–98.99 μM ranges. The predicted docked poses identified unique binding modes of the compounds and vital intermolecular interactions. The anti-microbial screening of the compounds were carried out against Escherichia coli, Bacillus subtillis, Staphylococcus aureus, Pseudomonas aeruginosa, Candida albicans and Aspergillus niger using agar well diffusion method. The standard drugs used were the anti-bacterial ciprofloxacin and the anti-fungal fluconazole. The compounds showed activity against all the microorganisms comparable to the used standard drugs. TPMC/EDA was more active than the standard fungal drug in the screening against the fungi strain, Aspergillus niger. It showed the MIC and IZD of 1.3 mg/ml and 9.0 mm respectively. These suggest that the compounds are potential bactericidal and fungicidal candidates.
Copper(I)-catalysed Regioselective Synthesis of Pyrazolo[5,1-c]-1,2,4-triazoles:
A DFT Mechanistic Study
D. Hallooman, H. Bhakhoa, M. Ríos-Gutiérrez, L. Rhyman, A. A. Oliferenko, A. R. Katritzky, I. A. Alswaidan, M. I. Elzagheid, L. R. Domingo and P. Ramasami
Tetrahedron, 2017, 73, 4653-4662
Formation of pyrazolo[5,1-c]-1,2,4-triazoles by means of Cu(I)-catalysed [3+2] cycloaddition (32CA) reactions of C,N-cyclic azomethine imines with phenylacetylene, experimentally reported by Katritzky et al. (JOC 2012, 77, 5813), was studied using the density functional theory (DFT) method. Comparison with the uncatalysed 32CA reaction indicates that the Cu(I) catalyst provides new reaction pathways with lower electronic energy barriers in dichloromethane as solvent. The mechanism proposed by Katritzky for the Cu(I) catalysed reaction is compared with that proposed by Sharpless et al. (JACS 127, 2005, 210). The major difference between these two mechanisms lies in the coordination of the Cu(I) acetylide to the C,N-cyclic azomethine imine moiety. DFT calculations suggest that the mechanism proposed by Katritzky is kinetically favoured over that of CuAAC-type. ELF topological analysis of the electron density of the stationary points involved in the most favourable reaction pathway associated with the Cu(I)-catalysed 32CA reactions explains the bond formation. This study also reveals the requirement of C,N-cyclic azomethine imines rather than acyclic azomethine imines to favour the mechanism proposed by Katritzky.
ExcelAutomat: A Tool for Systematic Processing of Files as
Applied to Quantum Chemical Calculations
J. Z. A. Laloo, N. Laloo, L. Rhyman and P. Ramasami
Journal of Computer-Aided Molecular Design, 2017, 31, 667-673
The processing of the input and output files of quantum chemical calculations often necessitates a spreadsheet as a key component of the workflow. Spreadsheet packages with a built-in programming language editor can automate the steps involved and thus provide a direct link between processing files and the spreadsheet. This helps to reduce user-interventions as well as the need to switch between different programs to carry out each step. The ExcelAutomat tool is the implementation of this method in Microsoft Excel (MS Excel) using the default Visual Basic for Application (VBA) programming language. The code in ExcelAutomat was adapted to work with the platform-independent open-source LibreOffice Calc, which also supports VBA. ExcelAutomat provides an interface through the spreadsheet to automate repetitive tasks such as merging input files, splitting, parsing and compiling data from output files, and generation of unique filenames. Selected extracted parameters can be retrieved as variables which can be included in custom codes for a tailored approach. ExcelAutomat works with Gaussian files and is adapted for use with other computational packages including the non-commercial GAMESS. ExcelAutomat is available as a downloadable MS Excel workbook or as a LibreOffice workbook.
Structural and Spectroscopic Parameters of CnF2+ (n = 1–5):
Insights using MP2/CBS Method
N. Toorabally, L. Rhyman, I. A. Alswaidan, C. Parlak, R. Somanah and P. Ramasami
Journal of Fluorine Chemistry, 2017, 200, 96-101
The structural and spectroscopic parameters of the fluorine doped carbon isomers, CnF2+ (n = 1–5) cations, were calculated using frozen core second order Møller-Plesset perturbation theory (MP2(fc)) at the complete basis set (CBS) limit with the aug-cc-pVXZ (X = D, T, Q) basis sets. The optimised geometries, rotational constants, dipole moments, and vibrational frequencies of the cations were computed to the CBS limit. The even-odd alternation effect was observed in the geometrical parameters, the dipole moments and the stabilities of the isomers. The carbon clusters containing even numbers of carbon atoms are linear with D∞h symmetry, while those containing an odd number of carbon atoms adopt a bent structure with bond angle in the range 120–130°. Some of the calculated parameters show good agreement to those available in the literature. Therefore, the reported data of the isomers should be accurate and it is hoped that the data on the isomers will be useful in helping to detect these cations in the interstellar medium.
Exploring the Potential Energy Surface of Novel [H, S, Se, Br] Species: A High Level First Principle Study
S. U. A. Ramjauny, I. A. Alswaidan, N. B. Jaufeerally-Safee, L. Rhyman and P. Ramasami
Journal of Molecular Modeling, 2017, In Press
The characterization of the seleno-sulfide-bromo systems and the isomerization process on the [H, S, Se, Br] potential energy surface were investigated using state-of-the-art theoretical methods. The CCSD(T) and the MP2 levels of theory were employed along with the series of correlation consistent basis sets extrapolated to the complete basis set (CBS) limit in the optimization of the geometrical parameters and computation of electronic energies. The relative stability, in kcal mol-1, at the CCSD(T)/CBS follows the trend: HSSeBr (0) > HSeSBr (9.51) > SSeHBr (24.02) > SeSHBr (25.42). This order was observed in the previous study of the [H, S, Se, Cl] species. The structural parameters and vibrational frequencies of the [H, S, Se, Br] species are reported. This research work should be helpful to experimentalists in order to gain insights into these novel heteroatom molecules.
TD-DFT Investigation of 2,5-Bis(2-benzothiazolyl)hydroquinone and
2,5-Bis(benzo[d]thiazol-2-yl)-4-methoxyphenol
M. M Jadhav, I. A. Alswaidan, L. Rhyman, P. Ramasami and N. Sekar
Journal of Solution Chemistry, 2017, 46, 1005–1023
Density functional theory (DFT) and time dependent density functional theory (TD-DFT) calculations of two excited state intramolecular proton transfer (ESIPT) molecules [2,5-bis(2-benzothiazolyl)hydroquinone and 2,5-bis(benzo[d]thiazol-2-yl)-4-methoxyphenol] were performed to study their structural and photo-physical behavior upon excitation. The most stable structure was established by optimizing all possible rotamers. The vertical excitation and emission wavelengths obtained by using TD-DFT show very good correlation with the experimental values. A correlation has been established based on the absorption values to determine the contribution of stable rotamers.
2,4-Ditellurouracil and its 5-Fluoro Derivative: Theoretical Investigations of Structural, Energetics and ADME Parameters
I. A. Alswaidan, K. Sooknah, L. Rhyman, C. Parlak, D. T. Ndinteh, M. I. Elzagheid
and P. Ramasami
Computational Biology and Chemistry, 2017, 68, 56-63
2,4-Ditellurouracil exhibits keto-enol tautomerism via different pathways resulting in seven tautomers. These pathways were studied in the gas phase using density functional theory method. The functionals used were BLYP, B3LYP and BHLYP and the basis sets were 6–311++G(d,p) for all atoms except that LanL2DZ ECP was used for tellurium atom only. The results indicate that the diketo form is more stable as observed for uracil and its sulfur and selenium analogues. The effect of introducing fluorine at position 5 was also investigated and the energy difference between the diketo and dienol forms is reduced. 2,4-Ditellurouracil and its 5-fluoro analogue are expected to exist exclusively as the diketo form due to the high interconversion energy barrier. We extended the investigation to predict ADME parameters of the most stable diketo and dienol tautomers in view of understanding their biological properties. This research enlightens keto-enol tautomerism of 2,4-ditellurouracil and its 5-fluoro derivative with additional insights to biological functions.
Triphenylamine-based Fluorescence Styryl Dyes:
DFT, TD-DFT and Non Linear Optical Property Study
S. Katariya, L. Rhyman, I. A. Alswaidan, P. Ramasami and N. Sekar
Journal of Fluorescence, 2017, 27, 993-1007
The electronic structures and spectroscopic properties of triphenylamine-based monostyryl and bis(styryl) dyes were studied using quantum chemical methods. The ground-state geometries of these dyes were optimized using the density functional theory (DFT) method. The lowest singlet excited state was optimized using time-dependent density functional theory (TD-DFT). The absorption was also calculated using the ground-state geometries. All the calculations were carried out in the gas phase and in solvent. The results indicate that the absorption maxima calculated using the TD-DFT are in good agreement with those obtained experimentally. These dyes possess a large second-order non-linear property and this is mainly due to the strong donor-π-acceptor conjugation which is attributed to the excited state intramolecular charge transfer (ICT). There is a relationship between the hardness and first hyperpolarizability and second hyperpolarizability of mono- and bis(styryl) dyes. The efficiency of the intersystem crossing process can be improved by reducing the energy gap between the singlet and triplet excited states.
Spectroscopic, DFT and XRD Studies of Hydrogen Bonds in
N-unsubstituted 2-aminobenzamides
M. J. Mphahlele, M. M. Maluleka, L. Rhyman, P. Ramasami and R. M. Mampa
The structures of the mono- and the dihalogenated N-unsubstituted 2-aminobenzamides were characterized by means of the spectroscopic (1H-NMR, UV-Vis, FT-IR, and FT-Raman) and X-ray crystallographic techniques complemented with a density functional theory (DFT) method. The hindered rotation of the C(O)–NH2 single bond resulted in non-equivalence of the amide protons and therefore two distinct resonances of different chemical shift values in the 1H-NMR spectra of these compounds were observed. 2-Amino-5-bromobenzamide (ABB) as a model confirmed the presence of strong intramolecular hydrogen bonds between oxygen and the amine hydrogen. However, intramolecular hydrogen bonding between the carbonyl oxygen and the amine protons was not observed in the solution phase due to a rapid exchange of these two protons with the solvent and fast rotation of the Ar–NH2 single bond. XRD also revealed the ability of the amide unit of these compounds to function as a hydrogen bond donor and acceptor simultaneously to form strong intermolecular hydrogen bonding between oxygen of one molecule and the NH moiety of the amine or amide group of the other molecule and between the amine nitrogen and the amide hydrogen of different molecules. DFT calculations using the B3LYP/6-311++G(d,p) basis set revealed that the conformer (A) with oxygen and 2-amine on the same side predominates possibly due to the formation of a six-membered intramolecular ring, which is assisted by hydrogen bonding as observed in the single crystal XRD structure.
Conformational and Electronic Properties of N-methacryloyl-(L)-glutamic Acid
C. Parlak, G. Keşan, N. Kazancı, L. Rhyman, P. Ramasami, Ö. Alver and S. Akgöl
Physics and Chemistry of Liquids, 2017, 55, 532-540
Conformers of N-methacryloyl-(L)-glutamic acid (MAGA, C9H13NO5) in the gas phase, benzene or methanol environment were searched by the density functional theory (DFT) and time-dependent DFT. Selected conformational isomers based on potential energy surface analysis were studied by considering the structural and electronic properties. B3LYP functional, and HF and MP2 levels were used with the 6-31+G(d,p), 6-311+G(3df,p) and aug-cc-pVDZ basis sets. We explored the effect of medium on the conformational preferences, UV spectra and frontier molecular orbitals of the conformers. The outcomes of this research will be useful for future studies including moieties analogous to MAGA.
A Fluoro-chromogenic Sensor Based on Organic Molecular Framework for Cu2+ and F– in Aqueous Soluble DMSO
V. Uahengo, Y. Zhang, B. Xiong, P. Zhao, P. Cai, L. Rhyman, P. Ramasami, K. Hu
and G. Cheng
Journal of Fluorescence, 2017, 27, 191-197
The 2,2′-dinaphtholazobenzene molecular framework (P) was designed, synthesized and characterized. Its absorption and fluorescence properties revealed that P is a dual sensor for copper ions (Cu2+) and fluoride ions (F−) in DMSO. The colorimetric activities were clearly visible by naked eye upon the addition of the two ions. Fluorescence quenching and enhancement were observed when Cu2+ and F− ions were added respectively. Density Functional Theory (DFT) calculations were carried out to provide an insight into the interaction of guest ions (Cu2+ and F−) with P, and to explain how the molecular orbitals were affected.
Internal Rotation of 2-, 3- and 4- Pyridine Carboxaldehydes and their Chalcogen Analogues (S and Se) in the Gas and Solution Phases: A Theoretical Investigation
H. H. Abdallah, P. H. Yeoh, L. Rhyman, I. A. Alswaidan, H.-K. Fun, Y. Umar
and P. Ramasami
Journal of Solution Chemistry, 2016, 45, 1195-1212
The optimized molecular structures, vibrational wavenumbers and corresponding vibrational assignments of the syn and anti conformers of 2-, 3- and 4-pyridine carboxaldehydes and their sulfur and selenium analogues were calculated using the density functional theory method employing the B3LYP functional with the 6-311++G(d,p) basis set and second order Møller–Plesset Perturbation Theory (MP2) method with the cc-pVDZ basis set. The calculations were adapted to the Cs symmetries of all ground state structures. The transition state arising from syn-anti isomerization was also modelled. All structures were fully optimized, and the geometries, rotational constants, dipole moments, charges, thermodynamic properties and energies are reported. Energies of the optimized structures were used to obtain the energy difference between the syn and anti conformers and the rotational barrier. The calculated vibrational wavenumbers were appropriately assigned to the various fundamental modes of vibrations. The Integral Equation Formalism Polarization Continuum Model was used to calculate the optimized geometry and the vibrational wavenumbers for all of the compounds in nine solvents: heptane, chloroform, tetrahydrofuran, dichloroethane, acetone, ethanol, methanol, dimethylsulfoxide and water. In addition, the LUMO, HOMO and energy band gap are also reported. The results indicate that the anti conformer is preferred with a rotational barrier of at least 19 kJ·mol−1.
Comprehensive DFT and TD-DFT Studies on the Photophysical Properties of 5,6-Dichloro-1,3-Bis(2-Pyridylimino)-4,7-Dihydroxyisoindole:
A New Class of ESIPT Fluorophore
S. Kataria, L. Rhyman, P. Ramasami and N. Sekar
Journal of Fluorescence, 2016, 26, 1805-1812
Hanson et al. [Org. Lett., 2011] reported the absorption and emission spectrum of 5,6-dichloro-1,3-bis(2-pyridylimino)-4,7-dihydroxyisoindole but the excited-state intramolecular proton transfer (ESIPT) process was not investigated. The photo-physical behaviour of 5,6-dichloro-1,3-bis(2-pyridylimino)-4,7-dihydroxyisoindole was studied using the density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The functional used was B3LYP and 6-31G(d) was the basis set for all the atoms. All the ten tautomers were studied for the absorption and emission properties. It is found that the tautomer where hydroxyl groups are syn to nitrogen of isoindoline ring is most stable and thus, responsible for the ESIPT process. The computed absorption and emission values of tautomers using TD-DFT are in good agreement with those obtained experimentally.
Unfolding ESIPT in Bis-2,5-(2-benzoxazolyl) Hydroquinone and 2,5-Bis(benzo[d]oxazol-2-yl)-4-methoxyphenol:
A Comprehensive Computational Approach
M. M. Jadhav, L. Rhyman, P. Ramasami and N. Sekar
Journal of Fluorescence, 2016, 26, 1295-1307
The photo-physical behaviour of bis-2,5-(2-benzoxazolyl) hydroquinone and 2,5-bis (benzo[d]oxazol-2-yl)-4-methoxyphenol was studied using the Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT). All the possible rotamers were optimized to obtain global minimum optimized structure. The theoretical absorption and emission values of rotamers estimated by using TD-DFT [TD-B3LYP/6–31G(d)] are in good agreement with experimental absorption and emission wavelengths. Based on the absorption values, the contribution of respective rotamer is determined theoretically.
1-Formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline:
Synthesis, Characterization, Antimicrobial Activity and DFT Studies
A. Sid, A. Messai, C. Parlak, N. Kazancı, D. Luneau, G. Keşan, L. Rhyman, I. A. Alswaidan and P. Ramasami
Journal of Molecular Structure, 2016, 1121, 46-53
The structure of 1-formyl-3-phenyl-5-(4-isopropylphenyl)-2-pyrazoline synthesized as single crystal was investigated by FTIR, NMR, XRD. Experimental data were complemented by quantum mechanical calculations. XRD data show that the compound crystallizes in the triclinic system (P−1) via trans isomer (a = 6.4267(4) Å, b = 10.9259(12) Å, c = 12.4628(9) Å and α = 102.894(8)°, β = 102.535(6)°, γ = 101.633(7)°). Anti-microbial screening results indicate that the compound shows promising activity. The theoretically predicted and experimentally obtained parameters reveal further insight into pyrazoline systems.
Synthesis, Characterization, Antimicrobial Screening and Computational Studies of 4-[3-(4-Methoxy-phenyl)-allylideneamino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one
L. N. Obasi, G. U. Kaior, L. Rhyman, I. A. Alswaidan, H.-K. Fun and P. Ramasami
Journal of Molecular Structure, 2016, 1120, 180-186
The Schiff base, 4-[3-(4-methoxy-phenyl)-allylideneamino]-1,5-dimethyl-2-phenyl-1,2-dihydro-pyrazol-3-one (TPMC/AAP) was synthesized by the condensation of 4-aminoantipyrine (4-amino-1,5-dimethyl-2-phenylpyrazole-3-one) and trans-para-methoxycinnamaldehyde (trans-3,4-methoxyphenyl-2-propenal) in dry methanol at 75 °C. The compound was characterized using elemental microanalysis, IR, NMR, UV spectroscopies and single-crystal X-ray crystallography. The X-ray structure determination shows that the Schiff base, (TPMC/AAP) is orthorhombic with the Pbca space group. The anti-microbial screening of the compound was carried out with Escherichia coli, Bacillus subtillis, Staphylococcus aureus, Pseudemonas aeruginosa, Candida albicans and Aspergillus niger using agar well diffusion method. The Schiff base possesses significant antimicrobial activity. The minimum inhibitory concentration (MIC) of the compound was also determined and the activity was compared with that of conventional drugs ciprofloxacin and ketoconazole. The compound (TPMC/AAP) showed varying activity against the cultured bacteria and fungi used. To complement the experimental data, density functional theory (DFT) was used to have deeper understanding into the molecular parameters and infrared spectra of the compound.
[3+2] Cycloaddition Reaction of 1H-Phosphorinium-3-olate and
1-Methylphosphorinium-3-olate with Methyl Acrylate: A DFT Study
D. Hallooman, M. Ríos-Gutiérrez, L. Rhyman, I. A. Alswaidan, H.-K. Fun, L. R. Domingo and P. Ramasami
Computational and Theoretical Chemistry, 2016, 1087, 36-47
A density functional theory study was performed on the [3+2] cycloaddition (32CA) reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl acrylate. The thermodynamic and kinetic parameters were analysed by considering the regio- and stereoisomeric pathways in gas phase and solvents. The geometries indicate that the transition states are slightly more advanced and asynchronous in ethanol. Electron localisation function topological analysis of the bonding changes along the most favourable reaction path associated with the 32CA reaction of 1H-phosphorinium-3-olate with methyl acrylate indicates that the reaction takes place through a two-stage one-step mechanism. Non-covalent interactions analysis of TS6x-H reveals the existence of weak hydrogen bonding explaining the regioselectivity found in this low-polar zw-type 32CA reaction. On comparing these theoretical findings with the nitrogen analogues of the 32CA reactions, it is found that the regioselectivity is affected and the pathways are kinetically and thermodynamically enhanced. Therefore, a priori, the phosphorus cycloadducts could be synthesised.
Discovery of Anti-Ebola Drugs: A Computational Drug Repositioning Case Study
P. S. Kharkar, P. Ramasami, Y. S. Choong, L. Rhyman and S. Warrier
RSC Advances, 2016, 6, 26329-26340
Computational drug repositioning has complemented and guided the experimental drug repositioning assignments in the recent past. Structure- and ligand-based strategies have been tried for the generation of novel repositioning ideas. In the present computational work, an attempt has been made to reposition a set of approved/existing drugs as novel anti-Ebola agents, targeting VP35 viral protein. One of the crystal structure ligands bound to VP35 protein was used as a query for the initial shape- and electrostatics-based virtual screening using OpenEye Scientific Software suite. The top-ranking hits from the ligand-based virtual screening were further docked in the ligand-binding pocket of the VP35 protein. The virtual hits from both the ligand- and structure-based screening were examined carefully in terms of tightness of their binding interactions with the macromolecular target. Several top hits belonged to therapeutic categories like antidiabetics (e.g., nateglinide), antihypertensives (e.g., telmisartan) and antibiotics (e.g., ticarcillin), etc., totally unrelated to the proposed antiviral indication. The computational repositioning hypotheses generated at the end of this study are likely to interest several researchers around the globe that are desperately looking for a breakthrough treatment to curb the recent menace created by a relatively older virus. The proposed hits that are approved/existing drugs may serve as starting points for the clinical repositioning for anti-Ebola indication or as lead structures in fast-track anti-Ebola drug discovery campaigns.
Effective Adsorption of Pyridine (Py) – onto Mesoporous Silica Derived from
De-oiled Mustard Cake (DOMC): Experimental and Theoretical Study
B. Chandra, L. Rhyman, P. Ramasami and K. Singh
Journal of Environmental Chemical Engineering, 2016, 4, 1383-1392
Effective adsorption of pyridine (Py)- a major pollutant present in various industrial wastewaters onto silica derived from de-oiled mustard cake (DOMC) was evaluated. Fourier transform infrared spectroscopy (FT-IR) and SEM were used to characterized the adsorbent. The paper describes data on the chemical composition of the DOMC, kinetics and equilibrium adsorption of Py as well as the effect of different operational parameters (temperature, pH, ionic strength and effect of urea) on the effective removal of Py from its aqueous solution. Adsorption data were modeled with the Freundlich, Langmuir, Redlich–Peterson (R–P) and Temkin isotherm. The adsorption data are found suitable for the studied models quite reasonably. However, the results describe the best representation of the Langmuir isotherm model (non-linear R2 = 0.99). The adsorption process followed Lagergren first order kinetics. The experimental findings were complemented using density functional theory (DFT) to have more understanding at atomistic level. The possible adsorption interactions were discussed. The effects of process parameters such as pH, urea and ionic strength on the adsorption suggested that the adsorption of Py was attributed to hydrogen bonding; however, hydrophobic interactions and charge transfer interactions are also believed to be responsible for the observed adsorption in the present case. The experimental data were subsentiated by employing a silica model based on DFT. Experimental and theoretical modeling of the adsorption phenomenon suggest hydrogen bonding to be a dominant force for Py adsorption onto silica.
Can Cyclen Bind Alkali Metal Azides? A DFT Study as a Precursor to Synthesis
H. Bhakhoa, L. Rhyman, Ed P. F. Lee, P. Ramasami and J. M. Dyke
Chemistry – A European Journal, 2016, 22, 4469-4482
Can cyclen (1,4,7,10-tetraazacyclododecane) bind alkali metal azides? This question is addressed by studying the geometric and electronic structures of the alkali metal azide-cyclen [M(cyclen)N3] complexes using density functional theory (DFT). The effects of adding a second cyclen ring to form the sandwich alkali metal azide-cyclen [M(cyclen)2N3] complexes are also investigated. N3− is found to bind to a M+(cyclen) template to give both end-on and side-on structures. In the end-on structures, the terminal nitrogen atom of the azide group (N1) bonds to the metal as well as to a hydrogen atom of the cyclen ring through a hydrogen bond in an end-on configuration to the cyclen ring. In the side-on structures, the N3 unit is bonded (in a side-on configuration to the cyclen ring) to the metal through the terminal nitrogen atom of the azide group (N1), and through the other terminal nitrogen atom (N3) of the azide group by a hydrogen bond to a hydrogen atom of the cyclen ring. For all the alkali metals, the N3-side-on structure is lowest in energy. Addition of a second cyclen unit to [M(cyclen)N3] to form the sandwich compounds [M(cyclen)2N3] causes the bond strength between the metal and the N3 unit to decrease. It is hoped that this computational study will be a precursor to the synthesis and experimental study of these new macrocyclic compounds; structural parameters and infrared spectra were computed, which will assist future experimental work.
Ion-Pair SN2 Substitution: Activation Strain Analyses of Counter-Ion and
Solvent Effects
J. Z. A. Laloo, L. Rhyman, P. Ramasami, M. F. Bickelhaupt and A. de Cózar
Chemistry – A European Journal, 2016, 22, 4431-4439
The ion-pair SN2 reactions of model systems MnFn−1+CH3Cl (M+=Li+, Na+, K+, and MgCl+; n=0, 1) have been quantum chemically explored by using DFT at the OLYP/6-31++G(d,p) level. The purpose of this study is threefold: 1) to elucidate how the counterion M+ modifies ion-pair SN2 reactivity relative to the parent reaction F−+CH3Cl; 2) to determine how this influences stereochemical competition between the backside and frontside attacks; and 3) to examine the effect of solvation on these ion-pair SN2 pathways. Trends in reactivity are analyzed and explained by using the activation strain model (ASM) of chemical reactivity. The ASM has been extended to treat reactivity in solution. These findings contribute to a more rational design of tailor-made substitution reactions.
Synthesis, Photophysical Properties and DFT Study of Novel Polycarbo-substituted Quinazolines Derived from the 2-Aryl-6-bromo-4-chloro-8-iodoquinazolines
H. P. Paumo, M. J. Mphahlele, L. Rhyman and P. Ramasami
Tetrahedron, 2016, 72, 123-133
A series of novel 2-aryl-6-bromo-4-chloro-8-iodoquinazolines were prepared and subjected to sequential two-step (Sonogashira and subsequent one-pot bis-Suzuki) and one-pot three-step Sonogashira cross-coupling reactions to afford unsymmetrical polycarbo-substituted quinazolines. Selectivity in the cross-coupling for these multihalogenated quinazolines was found to depend on both the intrinsic reactivity of the Csp2–halogen bond, which relates to the bond dissociation energy or bond strength and the electronic position of the halogen atom on the electron deficient scaffold (trend: Csp2–I>C(4)–Cl>Csp2–Br). The electronic absorption and emission properties of the prepared polycarbo-substituted quinazolines were evaluated in solution by means of UV–Vis and emission spectroscopy in conjunction with density functional theory (DFT) method.
Chromogenic Signaling of Water Traces by 1,8-Naphthalohydrazone-anion
Complex in Organic Solvents
V. Uahengo, B. Xiong, P. Cai, L. S. Daniel, L. Rhyman and P. Ramasami
Analytical Chemistry Research, 2016, 8, 1-8
A naphthalo-1, 8-bis[(2,4-dinitrophenyl)hydrazone] sensor (K) was synthesized and characterized using UV–vis, 1H NMR and fluorescence spectroscopy. The sensor showed strong colorimetric and spectral response upon the molar addition of acetate or fluoride ion (AcO− or F−) in acetonitrile. The complexed state (KF or KAcO) of the system showed significant reversibility properties, both in color and spectra, upon the addition of small traces of water. Subsequently, in addition to sensing of fluoride or acetate ions, the complexed KF or KAcO adducts can be used in colorimetric signaling of water traces in different organic mediums. In order to have more understanding of the interaction between K and the anions, the study was supplemented using density functional theory computations.
Dioxidomolybdenum(VI) Complexes of Allyl N’-2-Hydroxy-3-methoxybenzylidenecarbamohydrazonothioate:
Synthesis, Spectral and Theoretical Investigation
R. Takjoo, P. Ramasami, J. T. Mague, Z. Hasani and L. Rhyman
Journal of Coordination Chemistry, 2016, 69, 1100-1109
The new dibasic NNO ligand H2L (H2L = allyl N′-2-hydroxy-3-methoxybenzylidenecarbamohydrazonothioate) was synthesized by condensation of 2-hydroxy-3-methoxybenzaldehyde with the product resulting from the reaction of thiosemicarbazide with allyl bromide. Four dioxidomolybdenum(VI) complexes with the general formula [MoO2L(S)] (S=MeOH, EtOH, DMSO, and 1-methylimidazole) were synthesized and characterized by elemental analysis, FT-IR, EI-MS and UV-Vis spectroscopy, and by X-ray crystallography. Spectroscopic evidence indicates that the cis-MoO2 chelates have octahedral geometry in which H2L coordinates via the phenolate oxygen, azomethine nitrogen and deprotonated thioamide nitrogen. The other sites are occupied by two oxido and an additional ligand (S). Density functional theory calculations of spectral parameters were also carried out for these systems.
Ultrasound-assisted Chiral Derivatization of Etodolac with (1R)-(-)-Menthyl Chloroformate for the Determination of Etodolac Enantiomers
Y. Jin, J. Zhao, L. Rhyman, P. Ramasami, Y. Shin, K. Min Jeong and J. Lee
Arabian Journal of Chemistry, 2016, 9, S1962–S1972
This study presents the first report of an ultrasound-assisted derivatization reaction between a carboxylic acid of etodolac (ETO) and a chiral derivatization reagent, (1R)-(−)-menthyl chloroformate (R-MCF). Fifty μL of deproteinated mouse serum containing ETO enantiomers was derivatized with 125 μL of 200 mM R-MCF and 17 μL of pyridine (a catalyst), with the reaction facilitated by ultrasonic radiation for 13 min, which were the optimal conditions as determined by response surface methodology. After quenching the reaction by adding an aqueous L-proline solution, the mixture was subjected to salting-out assisted liquid–liquid extraction (SA-LLE), which provided phase separation for sample concentration as well as cleanup. The ETO diastereomers were separated on a Phenomenex Gemini C18 column (150 × 4.6 mm, 5 μm) under a simple gradient elution of a mobile phase containing a mixture of methanol: acetonitrile (10:1, V/V) and 10 mM acetic acid at a flow rate of 1.0 mL min−1, followed by fluorescence detection with excitation and fluorescence emission wavelengths of 235 nm and 345 nm, respectively. The developed method was validated for specificity, sensitivity, linearity, accuracy, precision, stability, and matrix effect. A good linearity in the range of 0.5–50.0 μg mL−1 for each ETO enantiomer with r2 > 0.998 and acceptable values for the intra-day and inter-day accuracy and precision as well as negligible matrix effects supported the suitability and reliability of the method. Finally, this method was used to analyze real samples taken from mice treated with (±)-ETO.
Fluorescent Difluoroboron-Curcumin Analogues: An Investigation of the Electronic Structures and Photophysical Properties
S. N. Margar, L. Rhyman, P. Ramasami and N. Sekar
Spectrochimica Acta, Part A: Molecular and Bimolecular Spectroscopy, 2016, 152, 241-251
A comprehensive approach based on the density functional theory method was used to elicit the molecular and photophysical properties of four difluoroboron analogs of curcumin. The ground state geometry optimization, vertical absorption and the first excited state optimization were carried out using the B3LYP/6-31G(d) method. The geometry of the molecules remains planar both in the ground and excited states. There is a good correlation between the observed absorption (maximum deviation of 8%) and emission wavelength (maximum deviation of 22%) with the computed values. Different polarizability parameters were computed and compared with urea. The values obtained for the difluoroboron dyes are larger than those of urea, suggesting considerable charge transfer characteristics of the first excited state. This is further supported by the significant difference in the dipole moment. The outcome of this work should be useful towards the industrial applications of these curcumin-based dyes.
Ab initio Studies on Cyanoacetylenes of Astrochemical Interest: [Y(C≡C)CN, Y = C2H5, C3H7, C4H9, F, Cl, Br and CN
D. Kodi Ramanah, P. Surajbali, L. Rhyman, I. A. Alswaidan, H.-K. Fun,
R. Somanah and P. Ramasami
New Astronomy, 2016, 42, 42-48
Theoretical studies were performed on seven potential interstellar and circumstellar substituted cyanoacetylenes, Y(CC)CN [Y = C2H5, C3H7, C4H9, F, Cl, Br and CN]. Geometry optimizations were carried out using the DFT/B3LYP, the CCSD and CCSD(T) levels of theory. The cc-pVTZ basis set was used for all atoms. Frequency computations were also carried out at the same level of theory as for the optimization to check the nature of the stationary points. The molecular and spectroscopic parameters of the cyanoacetylenes were computed. An analysis of these parameters is in line with the satisfactory performance of the B3LYP/cc-pVTZ level compared to the golden standard, the CCSD(T) level. The theoretical data reported in this work should facilitate future identifications of these cyanoacetylenes in extraterrestrial locations. Plausible mechanisms for the formation of these molecules have been proposed.
Halogen and Solvent Effects on the Conformational, Vibrational and Electronic Properties of 1,4-Diformylpiperazine: A Combined Experimental and DFT Study
C. Parlak, M. Tursun, C. S. Chidan Kumar, D. Bilge, N. Kazanci,
L. Rhyman and P. Ramasami
Journal of Theoretical and Computational Chemistry, 2015, 14
The molecular structure and properties of 1,4-diformylpiperazine (1,4-dfp, C6H1010N2O2) were investigated by Fourier transform infrared (FT-IR) spectroscopy, Raman spectroscopy and density functional theory (DFT). The Becke-3-Lee–Yang–Parr (B3LYP) functional was used with the 6-31++G(d,p) basis set. Total energy distribution (TED) analysis of normal modes was performed to identify characteristic frequencies by the scaled quantum mechanical (SQM) method. Halogeno-analogs of 1,4-dfp were studied to understand the halogen effect. Computations were focused on five conformational isomers of the compounds in the gas phase and in solutions. The computed and experimental frequencies of the C==O stretching vibration of 1,4-dfp were correlated with the empirical solvent parameters such as the Kirkwood–Bauer–Magat (KBM) equation, the solvent acceptor number (AN), Swain parameters and linear solvation energy relationships (LSER). The electronic properties of the compounds were also examined. The findings from the present work may be useful to understand systems involving the halogens and conformational changes analogous to the compounds investigated.
Structural, Spectroscopic and Energetic Parameters of P-bearing Species having Astrophysical Importance
K. Gooniah, H. Jhurree, L. Rhyman, I. A. Alswaidan, H.-K. Fun,
R. Somanah and P. Ramasami
Molecular parameters such as equilibrium structure, dipole moment, rotational constant, harmonic frequency, IR intensity, adiabatic electron affinity, atomisation energy and ionisation potential of some P-bearing molecules PS, PO and HC3P in their neutral, cationic and anionic forms were investigated using the popular B3LYP hybrid density functional with four basis sets 6-311++G(2df,2pd), 6-311++G(3df,3pd), cc-pVTZ and aug-cc-pVTZ. The computed data conform well to those existing in the literature. Therefore, the predicted data for those molecules or ions which are not available in the literature should be reliable.
Diels-Alderase Catalysing the Cyclisation Step in the Biosynthesis of Spinosyn A: Reality or Fantasy?
L. R. Domingo, J. A. Sáez, L. Rhyman and P. Ramasami
The conversion of putative macrocyclic lactone into the tricyclic compound, as a key step in the biosynthesis of spinosyn A reported by Kim et al. (Nature, 2011, 473, 109), has been theoretically investigated using DFT methods. The relatively low activation free energy computed for the cyclisation process of the actual macrocyclic lactone, 21.0 kcal/mol, furnishes a rationalisation for a spontaneous (i.e. non-enzymatically catalysed) cyclisation process in the biosynthesis of spinosyn A. A geometrical analysis of putative macrocyclic lactone indicates that a slight strain on the lactone at the active site of the SpnF gene could decrease the activation free energy to ca. 16 kcal/mol. This non-specific participation of the enzyme, which accounts for the relatively low 500-fold acceleration that Kim et al. found in this gene, rules out the participation a specific Diels-Alderase.
Synthesis and Photophysical Properties of Polycarbo-Substituted Quinazolines Derived from the 2-Aryl-4-chloro-6-iodoquinazolines
M. J. Mphahlele, H. K. Paumo, L. Rhyman and P. Ramasami
Molecules – Special Issue Heterocyclic Compounds, 2015, 20, 14656-14683
The reactivity of the 2-aryl-4-chloro-6-iodoquinazolines towards palladium catalyzed sequential (Sonogashira/Suzuki-Miyaura) and one-pot two-step cross-coupling (bis-Sonogashira, and successive Sonogashira/Stille) reactions to afford novel unsymmetrical polycarbo-substituted quinazolines has been evaluated. In contrast to the chloro-bromo substituted quinazolines in which selectivity has been previously found to generally favor substitution at the more activated C(4)-Cl bond over the weaker Csp2-Br bond, substitution in the case of the chloro-iodo derivatives favors cross-coupling through the intrinsically more reactive Csp2-I bond. The electronic absorption and emission properties of the prepared 2,3-diaryl-6-(phenylethynyl)quinazolines were studied in solvents of different polarity (dichloromethane, toluene, DMF, methanol) and CH2Cl2-TFA mixture using UV-Vis and emission spectroscopic techniques complemented with density functional theory method to establish the effect of substituents on intramolecular charge transfer properties.
Red Emitting Coumarins: Insights of Photophysical Properties with DFT Methods
A. B. Tathe, L. Rhyman, P. Ramasami and N. Sekar
Journal of Fluorescence, 2015, 25, 1117-1126
Red emitting dyes are of interest in various technological applications. Coumarins, though being an important class of fluorescent molecules, those with red emission, have been rarely studied theoretically. The structural and electronic aspects of three novel red emitting coumarins were studied using DFT and TD-DFT methods. The functionals employed were the hybrid functionals B3LYP, CAM-B3LYP, PBE0 and the highly parameterized empirical functional M06. The geometry at ground state reveals the electron donor N,N-diethylamino group is coplanar with the chromophoric system and the nitrile group induces a red shift to the absorption and emission. The electronic energies and dipole moments were solvent dependent. The basis sets and functionals were benchmarked for their performance with these molecules. B3LYP has been proved to be more efficient in computations whereas the basis sets do not have noticeable effect on the electronic properties. However, adding a polarization function to the basis set has improved the calculation of vertical excitation. The B3LYP functional gives maximum absolute deviation of 0.20 eV in calculating the vertical excitations and 0.18 eV for emission.
Aza-macrocyclic Complexes of the Group 1 cations – Synthesis, Structures and Density Functional Theory Study
J. M. Dyke, W. Levason, M. E. Light, D. Pugh, G. Reid, H. Bhakhoa,
P. Ramasami and L. Rhyman
Dalton Transactions, 2015, 44, 13853-13866
The Group 1 complexes, [M(Me6[18]aneN6)][BArF] (M = Li–Cs; Me6[18]aneN6 = 1,4,7,10,13,16-hexamethyl-1,4,7,10,13,16-hexaazacyclooctadecane; BArF = tetrakis{3,5-bis(trifluoromethyl)-phenyl}borate), are obtained in high yield by reaction of the macrocycle with M[BArF] in anhydrous CH2Cl2 solution, and characterised spectroscopically (1H, 13C{1H}, 7Li, 23Na, and 133Cs NMR), by microanalysis and, for M = Li, K, and Rb, by single crystal X-ray analysis. The structures show N6-coordination to the metal ion; the small ionic radius for Li+ leads to a puckered conformation. In contrast, the K+ ion fits well into the N6 plane, with the [BArF]− anions above and below, leading to two K+ species in the asymmetric unit (a hexagonal planar [K(Me6[18]aneN6)]+ cation and a ‘[K(Me6[18]aneN6)(κ1-BArF)2]− anion’, with long axial K⋯F interactions). The Rb+ ion sits above the N6 plane, with two long axial Rb⋯F interactions in one cation and two long, mutually cis Rb⋯F interactions in the other. The unusual sandwich cations, [M(Me3tacn)2]+ (M = Na, K; distorted octahedral, N6 donor set) and half-sandwich cations [Li(Me3tacn)(thf)]+ (distorted tetrahedron, N3O donor set), [Li(Me4cyclen)(OH2)]+, and [Na(Me4cyclen)(thf)]+ (both distorted square pyramids with N4O donor sets) were also prepared (Me3tacn = 1,4,7-trimethyl-1,4,7-triazacyclononane, Me4cyclen = 1,4,7,10-tetramethyl-1,4,7,10-tetraazacyclododecane). Density functional theory (DFT) calculations, using the BP86 and B3LYP functionals, show that the accessibility of the [M(Me3tacn)2]+ sandwich cations depends strongly on the M+ ionic radius, such that it is sufficiently large to avoid steric clashing between the Me groups of the two rings, and small enough to avoid very acute N–M–N chelate angles. The calculations also show that coordination to the Group 1 cation involves significant donation of electron density from the p-orbitals on the N atoms of the macrocycle, rather than purely electrostatic interactions.
Conformational, Vibrational and Electronic Properties of
CH3(CH2)3CX2NH2 (X = H, F, Cl or Br): Halogen and Solvent Effects
C. Parlak, M. Gökce, M. Tursun, L. Rhyman and P. Ramasami
Journal of Theoretical and Computational Chemistry, 2015, 14
The effects of varying halogen and solvent, in terms of vibrational and electronic properties, on the different conformers of 1-pentanamine [CH3(CH2)4NH2] and 1,1-dihalogeno-pentan-1-amines [CH3(CH2)3CX2NH2; X = F, Cl or Br] were investigated by employing the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The B3LYP functional was used with the 6-31++G(d,p) basis set. Computations were focused on the 10 conformational isomers of the compounds in the gas phase and both in non-polar (benzene) and polar (methanol) solvents. The present work explores the effects of the halogen and the medium on the conformational preference, and geometrical parameter, dipole moment, NH2 vibrational frequency, UV spectrum, highest occupied and lowest unoccupied molecular orbitals (HOMO–LUMO) orbital and DOS diagram of the conformers. The atypical characteristics of fluorine and bromine affecting the electrical bandgap, chemical hardness, electronegativity, PDOS or OPDOS plots and the absorption band are observed correspondingly. The findings of this work can be useful to those systems involving changes in the conformations analogous to the compounds studied.
Novel Cyanide-bridged Heterometallic Two-Dimensional Complex of 3-Methylpyridazine: Synthesis, Crystallographical, Vibrational, Thermal and DFT Studies
K. Gör, M. Tursun, G. Keşan, G. S. Kürkçüoğlu, L. Rhyman, C. Parlak, P. Ramasami,
O. Z. Yeşilel and O. Büyükgüngör
Journal of Inorganic and Organometallic Polymers and Materials, 2015, 25, 1205-1217
A novel Cu/Pd heterometallic cyanide-bridged complex of 3-methylpyridazine (3-mpdz), [Cu(3-mpdz)2Pd(µ-CN)4]n, was synthesized and its structure was characterized by FT-IR, Raman, single-crystal X-ray diffraction and thermal/elemental analysis techniques. The conformers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the complex were examined by means of the density functional theory method, the Becke-3–Lee–Yang–Parr (B3LYP) functional and the LANL2DZ basis set. Reliable vibrational assignments were investigated by the potential energy distribution analysis. The complex crystallizes in the triclinic space group P-1 with the unit cell parameters a = 6.6836(4) Å, b = 7.7777(5) Å, c = 8.9009(6) Å, α = 113.573(5)°, β = 94.565(6)° and γ = 92.437(5)°. There is a good interplay between experimental and theoretical findings to understand the complex at molecular level. The synthesised complex with potential industrial applications will add to the literature of the cyanide-bridged tetracyanometallates.
Reaction of [ReIIICl3(t-BuNC)(PPh3)2] with Aniline Derivatives: Isolation of Imido-Re(V) Complexes and a Re(III) Complex Containing Iminobenzoquinonate as Ligand
X. Schoultz, T. I. A. Gerber, E. Hosten, R. Betz, L. Rhyman and P. Ramasami
The rhenium(V) complexes [ReCl3(t-BuNC)(L)(PPh3)] (1–3) were isolated by the reaction of trans-[ReIIICl3(t-BuNC)(PPh3)2] (t-BuNC = tert-butyl isocyanide) with the ligands H2L (H2L = aniline (1), o-phenylenediamine (2), anthranilic acid (3)). In all these complexes the dianionic ligands L are coordinated monodentately as the imide. However, unexpectedly, with 2-aminophenol the complexes [ReVCl2(t-BuNC)(L)(PPh3)2](ReO4) (4) and the novel [ReIIICl2(t-BuNC)(ibq)(PPh3)2] (5) (ibq− = 2-iminobenzoquinonate, the two-electron oxidized form of HL−) were identified as the products. These complexes were characterized by single crystal X-ray crystallography, 1H NMR spectrometry, IR and electronic spectroscopy, and cyclic voltammetry. To complement the experimental data, density functional theory (DFT) and time-dependent DFT methods were used to have a deeper understanding into the molecular parameters and infrared and electronic spectra of these complexes.
(2E)-1-(5-Chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one:
Synthesis, XRD, FT-IR, Raman and DFT Studies
C. Parlak, P. Ramasami, C. S. Chidan Kumar, M. Tursun, C. K. Quah, L. Rhyman, M. Bilge, H.-K. Fun and S. Chandraju
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015, 149, 385-395
A novel (2E)-1-(5-chlorothiophen-2-yl)-3-{4-[(E)-2-phenylethenyl]phenyl}prop-2-en-1-one [C21H15ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of HF, MP2, BP86, BLYP, BMK, B3LYP, B3PW91, B3P86 and M06-2X functionals. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the triclinic space group P-1 with the cis–trans–trans form. There is a good agreement between the experimentally determined structural parameters and vibrational frequencies of the compound and those predicted theoretically using the density functional theory with the BLYP and BP86 functionals.
Density Functional Theory Study of Cyanoetheneselenol:
A Molecule of Astrobiological Interest
P. Surajbali, D. Kodi Ramanah, L. Rhyman, R. Somanah and P. Ramasami
Origins of Life and Evolution of Biospheres, 2015, 45, 455-468
The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6–311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array.
DFT Studies of the Photophyscial Properties of Fluorescent and Semiconductor Polycyclic Benzimidazole Derivatives
U. Wardhe, L. Rhyman, N. Sekar and P. Ramasami
Journal of Fluorescence, 2015, 25, 685-694
The photophysical and electrochemical properties of eleven polycyclic benzimidazole fused organic pigments (four based on phthalic anhydride, four based on naphthalic anhydride and three based naphthalene tetra carboxylic acid dianhydride) were investigated using density functional theory and time dependent density functional theory methods (B3LYP/6-31G(d) and M06/6-31G(d)). The predicted geometries are comparable using both functionals. The electrochemical properties are in good agreement with the experimental results. However, the experimental absorption-emission properties are closer to the values computed using the M06/6-31G(d) method. Both the methods perform equally well in explaining the intramolecular charge transfer characteristics. This work can help to understand the modern age functional materials at molecular level and to design new molecules.
Crystal Structure, Vibrational Spectra and DFT Simulations
of 2-Fluoro-4-bromobenzaldehyde
M. Tursun, C. S. Chidan Kumar, M. Bilge, L. Rhyman, H.-K. Fun, C. Parlak,
P. Ramasami, S. Chandraju and C. K. Quah
Spectrochimica Acta, Part A: Molecular and Bimolecular Spectroscopy, 2015, 146, 342-349
Molecular structure and properties of 2-fluoro-4-bromobenzaldehyde (FBB, C7H4BrFO) was experimentally investigated by X-ray diffraction technique and vibrational spectroscopy. Experimental results on the molecular structure of FBB were supported with computational studies using the density functional theory, with the Becke-3-Lee–Yang–Parr functional and the 6-311+G(3df,p) basis set. Molecular dimer formed by the intermolecular hydrogen bonding was investigated. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. FBB crystallizes in orthorhombic space group P212121 with the O-trans conformation. In order to investigate halogen effect, the chloro- (CBB) and bromo- (BBB) analogs of FBB have also been studied theoretically. It is observed that all compounds prefer the stable O-trans conformation. Although the free energy difference between the O-cis and O-trans conformers is less than 2.5 kcal/mol, the free energy rotational barrier is at least 7.4 kcal/mol. There is a good agreement between the experimentally determined structural parameters, and vibrational frequencies of FBB and those predicted theoretically.
4-Mercaptophenylboronic acid:
Conformation, FT-IR, Raman, OH Stretching and Theoretical Studies
C. Parlak, P. Ramasami, M. Tursun, L. Rhyman, M. Fatih Kaya, N. Atar,
Ö. Alver and M. Şenyel
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015, 144, 131-138
4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives.
Sodium Thioether Macrocyclic Chemistry:
Remarkable Homoleptic Octathia Coordination to Na+
M. J. D. Champion, J. M. Dyke, W. Levason, M. E. Light, D. Pugh,
H. Bhakhoa, L. Rhyman, P. Ramasami and G. Reid
Inorganic Chemistry, 2015, 54, 2497-2499
Unprecedented homoleptic octathioether macrocyclic coordination to Na+ in [Na([24]aneS8)]+ has been achieved by using Na[B{3,5-(CF3)2-C6H3}4] as a source of “naked” Na+ ions and confirmed crystallographically, with d(Na–S) = 2.9561(15)–3.0524(15) Å. Density functional theory calculations show that there is electron transfer from the S 3p and C 2p valence orbitals of the ligand to the 3s and 3p orbitals of the Na+ ion upon complexation.
3-Iodobenzaldehyde: XRD, FT-IR, Raman and DFT studies
C. S. Chidan Kumar, C. Parlak, M. Tursun, H.-K. Fun, L. Rhyman, P. Ramasami,
I. A. Alswaidan, G. Keşan, S. Chandraju, C. K. Quah
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015, 145, 90-97
The structure of 3-iodobenzaldehyde (3IB) was characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The conformational isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of 3IB were examined using density functional theory (DFT) method, with the Becke-3-Lee-Yang-Parr (B3LYP) functional and the 6-311+G(3df,p) basis set for all atoms except for iodine. The LANL2DZ effective core basis set was used for iodine. Potential energy distribution (PED) analysis of normal modes was performed to identify characteristic frequencies. 3IB crystallizes in monoclinic space group P21/c with the O-trans form. There is a good agreement between the theoretically predicted structural parameters, and vibrational frequencies and those obtained experimentally. In order to understand halogen effect, 3-halogenobenzaldehyde [XC6H4CHO; X = F, Cl and Br] was also studied theoretically. The free energy difference between the isomers is small but the rotational barrier is about 8 kcal/mol. An atypical behavior of fluorine affecting conformational preference is observed.
Theoretical Insight into the Effect of Fluorine Substituents
on the Rearrangement Step in Fischer Indolisations
L. Rhyman, I. A. Alswaidan, H.-K. Fun, J. A. Joule and P. Ramasami
Special Issue of Tetrahedron: Memorial for Professor Katritzky,
Tetrahedron, 2015, 71, 7199-7203
Houk and coworkers clarified several aspects of the mechanism of the Fischer indole synthesis, showing that the SCS-MP2/6-31G(d)//MP2/6-31G(d) method is suitable for studying the mechanism in water. Fluorine substitution can affect the kinetic and thermodynamic parameters of a reaction, hence the work reported here considers the impact of fluorine substituents located on the ketone component of the starting phenylhydrazone in a Fischer indole synthesis. When one of the nitrogens is protonated, the presence of one fluorine decreases the activation energy of the key [3,3]-sigmatropic rearrangement and increases the thermodynamic stability of the resulting non-aromatic imine; the presence of two fluorines also reduces the activation energy versus the unsubstituted situation, but by a smaller amount. For a non-protonated sequence, although the presence of one fluorine again decreases the activation energy of the key [3,3]-sigmatropic rearrangement, inclusion of two fluorines actually increases the activation energy slightly.
Conformation and NH stretching of 1,1-Dihalogenoheptan-1-amines
[CH3(CH2)5CX2NH2; X = F, Cl or Br]: Halogen and Solvent Effects
M. Tursun, L. Rhyman, C. Parlak, P. Ramasami and M. Şenyel
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015, 139, 171-178
The effects of halogen and solvent on the conformation and NH stretching of 1,1-dihalogeno-heptan-1-amines [CH3(CH2)5CX2NH2; X = F, Cl or Br] were investigated using the density functional theory method. The functional used was B3LYP employing the 6-31++G(d,p) basis set for all atoms. Computations were carried out for ten possible conformational isomers of the compounds, in the gas phase and both in a non-polar solvent (benzene) and in a polar solvent (methanol). This research work indicates that both the halogen and the medium affect conformational preference, geometrical parameters and NH vibrational frequency. The findings of this work can be useful to those systems involving changes in the conformations analogous to the compounds studied.
Synthesis, Molecular Structure, FT-IR, Raman, XRD and Theoretical Investigations of (2E)-1-(5-Chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one
C. S. Chidan Kumar, H.-K. Fun, C. Parlak, L. Rhyman, P. Ramasami, M. Tursun,
S. Chandraju and C. K. Quah
Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2014, 132, 174-182
A novel (2E)-1-(5-chlorothiophen-2-yl)-3-(naphthalen-2-yl)prop-2-en-1-one [C17H11ClOS] compound has been synthesized and its structure has been characterized by FT-IR, Raman and single-crystal X-ray diffraction techniques. The isomers, optimized geometric parameters, normal mode frequencies and corresponding vibrational assignments of the compound have been examined by means of the density functional theory, the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution and natural bonding orbital analyses, respectively. The compound crystallizes in the monoclinic space group P21/c with the unit cell parameters a = 5.7827(8) Å, b = 14.590(2) Å, c = 16.138(2) Å and Z = 4. The C=C bond of the central enone group adopts an E configuration. There is a good agreement between the theoretically predicted structural parameters and vibrational frequencies and those obtained experimentally.
An Integrated Experimental and Theoretical Investigation of the Structural and Spectroscopic properties of two Nickel(II) Isothiosemicarbazone
R. Takjoo, P. Ramasami, A. Hashemzadeh, L. Rhyman, H. A. Rudbari and G. Bruno
Journal of Coordination Chemistry, 2014, 67, 1392-1404
Two novel nickel(II) isothiosemicarbazone complexes were synthesized, and were characterized by single crystal X-ray crystallography, 1H NMR spectrometry, IR and electronic spectroscopy. The complexes have square planar geometry and the ligand is coordinated to the metal ion as dinegatively charged tridentate chelating agents via phenolic oxygen, isothioamide nitrogen and azomethine nitrogen atoms. To complement the experimental data, density functional theory (DFT) and time-dependent DFT were used to validate the structural, molecular, infrared and electronic spectra.
4-Chloro-3-fluorobenzaldehyde: Experimental (XRD, FT-IR and Raman) and DFT Studies
C. Parlak, C. S. Chidan Kumar, H.-K. Fun, G. Keşan, L. Rhyman, P. Ramasami, S. Chandraju and C. K. Quah
Journal of Fluorine Chemistry, 2014, 163, 7-15
The structure of 4-chloro-3-fluorobenzaldehyde (CFB, C7H4ClFO) has been characterized by single crystal X-ray diffraction, FT-IR and Raman techniques. The conformational isomers, optimized geometrical parameters, normal mode frequencies and corresponding vibrational assignments of CFB have been examined using the density functional theory method, with the Becke-3-Lee-Yang-Parr functional and the 6-311+G(3df,p) basis set. Reliable vibrational assignments and molecular orbitals have been investigated by the potential energy distribution. CFB crystallizes in monoclinic space group P21/c with the O-cis conformation. In order to examine the effect of fluorine on the conformational preference, the chloro- and bromo- analogs of CFB have also been studied theoretically. It is observed that CFB prefers the O-cis conformation while the chloro- and bromo- analogs prefer the O-trans conformation. Although the free energy difference between the O-cis and O-trans conformers is less than 0.2 kcal/mol, the free energy rotational barrier is at least 8.4 kcal/mol [B3LYP/6-311+G(3df,p)]. MP2/aug-cc-pVDZ computations reveal that these free energies remain almost unaffected. The atypical characteristic of fluorine affecting conformational isomerism is observed. In addition, there is a good agreement between the experimentally determined structural parameters and vibrational frequencies of CFB and those predicted theoretically.
A Density Functional Theory Study of the Regio- and Stereoselectivity of the 1,3-Dipolar Cycloaddition of C-methyl Substituted Pyrazinium-3-olates with Methyl Acrylate and Methyl Methacrylate
L. Rhyman, P. Ramasami, J. A. Joule and L. R. Domingo
Computational and Theoretical Chemistry, 2013, 1025, 58-66
A DFT [B3LYP/6-31G(d)] study was carried out on the 1,3-dipolar cycloaddition (13DC) reactions of multi C-methyl substituted pyrazinium-3-olates with methyl acrylate (MA) and methyl methacrylate (MMA). Thermodynamic and kinetic parameters of the possible endo/exo stereoisomeric and 6-ester/7-ester regioisomeric pathways have been determined. The skeleton rearrangement of the 6-exo [3+2] cycloadducts into the [4+2] adducts is also considered. The electrophilic, , and nucleophilic, , Parr functions are used to have better understanding of the regioselectivity of these 13DC reactions. In all cases the exo pathways are more favorable compared to the endo alternatives. Inclusion of methyl groups at the C-2 and C-5 positions of pyrazinium-3-olate shows that the 7-exo cycloadduct is predicted to be the major product followed by its 6-exo isomer. These theoretical results have been compared with the previously reported studies on 13DCs of unsubstituted and substituted pyrazinium-3-olates with MA and MMA. The activation energy of these 13DCs ranges from 42.5 to 98.2 kJ mol-1 in THF.
A DFT Study of the [3 + 2] versus [4 + 2] Cycloaddition Reactions of 1,5,6-Trimethylpyrazinium-3-olate with Methyl Methacrylate
L. R. Domingo, J. A. Sáez, J. A. Joule, L. Rhyman and P. Ramasami
Journal of Organic Chemistry, 2013, 78, 1621-1629
The reaction between 1,5,6-trimethylpyrazinium-3-olate and methyl methacrylate (MMA) yielding a lactone–lactam has been studied using the DFT method at the B3LYP/6-31G(d) level. It is concluded that formation of the lactone–lactam is a domino process involving three consecutive reactions: (i) a 1,3-dipolar cycloaddition (13DC) reaction between the pyrazinium-3-olate and MMA yielding a [3 + 2] cycloadduct (CA); (ii) a skeletal rearrangement, which converts the [3 + 2] CA into a formal [4 + 2] CA, possessing a diazabicyclo[2.2.2]octane structure; and finally, (iii) an SN2 reaction, promoted by halide anion, with concomitant nucleophilic attack of the created carboxylate anion on an iminium carbon with formation of the lactone ring present in the lactone–lactam. Analysis of the four competitive channels associated with the 13DC reaction indicates that this cycloaddition takes place with complete endo stereoselectivity and 6 regioselectivity, yielding [3 + 2] CA. The subsequent skeletal rearrangement also takes place in an elementary step via a non-concerted mechanism. Electron localization function bonding analysis makes it possible to establish that the bicyclo[2.2.2]octane skeleton present in the lactone–lactam complex structure is not attained via a Diels–Alder reaction between pyrazinium-3-olate and MMA.
Structural and DFT/TD-DFT Investigation of Tris(bidentate) Complexes of Rhenium(III) Synthesized from the Cis-[ReO2]+ Core and Benzenethiol Derivatives
K. C. Potgieter, T. I. A. Gerber, R. Betz, L. Rhyman and P. Ramasami
The reaction of the rhenium(V) complex cis-[ReO2I(PPh3)2] with 2-aminothiophenol (H2atp), benzene-1,2-dithiol (H2tdt) and 2-hydroxybenzenethiol (H2otp) led to the formation of the rhenium(III) complexes [Re(Hatp)(ibsq)2]·OPPh3, [Re(sbsq)3]·OPPh3 and [Re(obsq)3]·OPPh3 (ibsq = 2-iminothiobenzosemiquinonate, sbsq = 1,2-dithiobenzosemiquinonate, obsq = 2-hydroxothiobenzosemiquinonate) respectively. These paramagnetic complexes were characterized by single crystal X-ray crystallography, 1H NMR spectrometry, IR and electronic spectroscopy, and cyclic voltammetry. To complement the experimental data, density functional theory (DFT) and time-dependent DFT were successfully used to investigate the structural, molecular, infrared and electronic spectra of these three complexes.
Understanding the Formation of [3+2] and [2+4] Cycloadducts in the Lewis Acid Catalysed Reaction Between Methyl Glyoxylate Oxime and Cyclopentadiene: A Theoretical Study
L. Rhyman, P. Ramasami, J. A. Joule, J. A. Sáez and L. R. Domingo
RSC Advances, 2013, 3, 447-457
The formation of the formal [3+2] and [2+4] cycloadducts in the Lewis acid (LA) catalysed reaction of cyclopentadiene (Cp, 1) with methyl glyoxylate oxime (MGO, 2a) has been theoretically studied using DFT methods. Coordination of BF3 LA to the oxygen atom of MGO 2a not only increases the electrophilicity of the oxime, but also makes the corresponding tautomeric BF3:nitrone complex 8b the reactive species. The reaction is characterised by the nucleophilic attack of Cp 1 on the carbon atom of the corresponding BF3:nitrone complex 8b. The subsequent ring closure at the end of the reaction allows the formation of the [3+2] or [2+4] cycloadducts. ELF bonding analysis of selected points on the intrinsic reaction coordinate of the two competitive endo paths enables us to establish that the formation of the formal [3+2] or [2+4] cycloadducts takes place through stereoisomeric transition state structures with a similar electronic structure.