INDO Method Research Articles

Diurnal Variation of Ambient NH3 in Relation with Agricultural Activities and Meteorological Factors at a Rural Site in North India

Ammonia is a chemically active gas which accelerates particulate matter formation by combining with nitrate (NO3−) and sulphate (SO42-) in acid cloud droplets, thereby reducing air quality. Since pre-industrial times, NH3 emissions have more than doubled globally, owing to increase in agricultural activities and fertilizer usage. In this study, ambient NH3 monitoring was done during selected periods on event basis in summer season (kharif crop) at a rural site of Jhajjar district of Haryana. Collected gaseous NH3 samples in absorbing solution (1.4ml H2SO4 in 1 litre water) at a flow rate of 1 LPM were prepared with the indo phenol-blue method and analyzed using spectrophotometer at 630nm. Here, we present the day-night variation in ambient NH3 concentrations emitted from various agricultural activities such as synthetic fertilizers, animal manure, biological N-fixation, the crop residue in the field after harvest, biomass burning, etcin relation with meteorological parameters. Its emission was recorded as 1 to 45; 63 to 190; 98 to 187 and 56 to 249 µg m-3 during sowing, fertilizer addition, grain filling and biomass burning respectively.Concentration during the sowing period i.e. 1 to 45 µg m-3can be considered as baseline values.Concentration of ambient NH3 reached itsmaxima at night and minima duringmidday.NH3 concentration was observed to be high during night time which might be due to reduced dispersion as the atmospheric conditions are stable at night. Concentration of NH3 is majorly influenced by wind speed and wind direction & its dependence on these meteorological parameters suggested a local source influence indicating that the nearbyagricultural fields might be the major NH3contributors at the observational site.This study suggests that the knowledge of NH3 levels measured at various stages can help in implementing N efficient management system and emissions can be reduced by minimizing the Nitrogen (N) input during different stages. These measurements are also helpful in making fertilizer policy, and guidelines for farmers.

Quantum-Chemical Study of the Influence of Substitution on Anti-Virus Activity of Hydroxyl Substituted Benzaldehydes and Related Compounds

Using the wave functions of the quantum chemical INDO method, the molecular electrostatic potential (MESP) of hydroxyl substituted benzaldehydes and related compounds exhibiting the ability to inhibit the reproduction of the herpes simplex virus type I has been calculated. It has been established that the degree of biological activity correlates not only with the magnitude of the proton-acceptor capacity of the substituted, but also with the geometry of biologically active molecules. The correspondence between the MESP values of hydroxyl groups and the effectiveness of the inhibitory ability of the investigated substitutions has been established.

Theoretical investigation of fluorescence properties of EDTA and DTPA substituted tetraphenylporphyrin molecules

The matrix elements of spin–orbit coupling operator (HSO) and non-adiabatic coupling operator (Ω) for the H2ATPP–EDTA and H2ATPP–DTPA molecules were calculated using INDO method. Rate constants of internal conversion and of intersystem crossing were calculated using the values of matrix elements of HSO and Ω operators and excitation energies both calculated with the ADC(2) and TDDFT methods and obtained from experimental data. Results of calculations show that the probability of radiationless deactivation in internal conversion channel is greater than the probability of radiationless transition in intersystem crossing channel for considered molecules. Obtained theoretical values of fluorescence quantum yield have good agreement with their experimental values.

A comparative study of the absorption spectra of o-aminophenols using different quantum-chemical methods

The electron-excited states of o-aminophenol and its derivatives are calculated using the INDO method with a special spectroscopic parametrization and the method based on the density functional theory (ADF code). The results of quantum-chemical calculations are compared with the absorption spectra of the compounds under study. It is found that the INDO method used for examination of the photophysics of organic molecules provides good results on the energies and intensities of radiation electron transitions in the foregoing compounds.

Quantum chemical investigation of spectral-luminescent properties of zwitterion and lactone forms of rhodamine B

A quantum chemical software package based on a semiempirical INDO method with original spectroscopic parameterization is used to calculate the electronically excited states of lactone and zwitterion forms of rhodamine B. The rate constants of photophysical processes are estimated, and the fluorescence quantum yields are calculated. It is established that the wave function of the S 1 state in the zwitterion form is localized on the pyronin fragment and delocalized throughout the molecule in the lactone form.

Quantum-chemical study of relation of spectral and luminescent properties of positively solvatochromic malononitrile-based merocyanine dyes with their structure

The electronic structure, the spectra, and the efficiency of photophysical processes of energy deactivation are calculated by a semiempirical method for three positively solvatochromic merocyanine dyes with different polymethine chain lengths. The electronic structure and spectra calculated by different modifications of the INDO method at different molecular geometries are compared, and the optimum geometry of the isolated molecule is chosen. The absorption spectra of dyes are interpreted, including the short-wave-length bands related to transitions to highest excited states. The possibility of a specific electrophilic solvation of these compounds in the ground and fluorescent states, as well as the contribution of specific intermolecular interactions to the total interaction with the medium, is estimated. The role played by the trans-cis isomerization of isolated merocyanine molecules in the deactivation of their excited states is considered.

Electronic structure and properties of model oxy and carboxy ferrous cytochrome P450: Comparison of semiempirical and ab-initio calculations

Semiempirical and ab-initio LCAO-MO-SCF calculations are reported for model oxy and carboxy ferrous cytochrome P450 with a methyl mercaptide SCH3− as an axial ligand for a number of conformations of the CO ligand and S-Fe-O-O torsion angle. For the semiempirical calculations a newly developed indo method including transition metal complexes is used with both a theoretical and a spectroscopic evaluation of one- and two-electron integrals. The electronic distributions obtained using the theoretical procedure compare well with the ab-initio results. Spectroscopic parametrization gives distributions and orbital energies which include some relaxation effects. The ground state description obtained with this parameterization yields values for the electric field gradient for both the oxy and the carboxy compounds which are in excellent agreement with experiment. Thus the anomalously large electric field gradient observed for the oxy and the extremely small electric field gradient observed for the carboxy P450 are both accounted for and support the validity of the calculated electronic structure.

Quantum chemical calculations on antipsychotic drugs and narcotic agents

Illustrative examples are given of comparative results on chlorpromazine by the cndo/2 method and by an indo method. For this we had previously extended the indo formalism to include d orbitals and parametrization to include compounds with second-row atoms. Results are presented for other antipsychotic drugs such as perazine and trifluoperazine and for the narcotic agent, morphine.

Satellite intensities in ESCA spectra of Ti(IV) fluoro- and oxocomplexes calculated by the multiple scattering and indo methods

Satellite intensities in the ESCA spectra of Ti(IV) compounds are calculated by the multiple scattering and indo cluster methods using a formula based on the sudden approximation. Only the next-nearest-neighbours (O or F) were included. The multiple scattering results indicate that both eg → e*g and t*2g → t*2g shake-up excitations contribute to the intensity of the satellite, whereas the indo results suggest that only eg → e*g contribute. A new result, and the most important one, is that the intensity ratio for the 3s satellite is as much as 50–70% of the intensity ratio for the 2p satellite.

A semi-empirical investigation of the electronic structure and stability of the oxycumulenes

A semiempirical investigation using the INDO and EWMO methods is carried out on the oxycumulenes in an attempt to explain the relative stabilities of the odd and even carbon compounds.

Molecular orbital calculations of the long-range proton-proton coupling constants in purine and pyrimidine nucleosides

The molecular orbital INDO method is used for the calculation of long-range NMR proton-proton coupling constants between H1, and protons of the base and between the protons of the furanose ring in purine and pyrimidine nucleosides. The computations show that the couplings between H1, and the protons of the base are negligible in the purine nucleosides and are very sensitive to the torsion angle about the glycosidic bond in pyrimidine nucleosides. For uridine and its derivatives the calculated J 1, 5 are in agreement with experiment for an anti conformation of these compounds. For α- and β-pseudouridines, J1, 6 is important and may be large for anti as well as syn conformations. The long-range couplings between the protons of the furanose ring vary little with the puckering of the sugar.

Fortran 90 implementation of the Hartree–Fock approach within the CNDO/2 and INDO models

Despite the tremendous advances made by the ab initio theory of electronic structure of atoms and molecules, its applications are still not possible for very large systems. Therefore, semi-empirical model Hamiltonians based on the zero-differential overlap (ZDO) approach such as the Pariser–Parr–Pople, CNDO, INDO, etc. provide attractive, and computationally tractable, alternatives to the ab initio treatment of large systems. In this paper we describe a Fortran 90 computer program developed by us, that uses CNDO/2 and INDO methods to solve Hartree–Fock (HF) equation for molecular systems. The INDO method can be used for the molecules containing the first-row atoms, while the CNDO/2 method is applicable to those containing both the first-, and the second-row, atoms. We have paid particular attention to computational efficiency while developing the code, and, therefore, it allows us to perform calculations on large molecules such as C 60 on small computers within a matter of seconds. Besides being able to compute the molecular orbitals and total energies, our code is also able to compute properties such as the electric dipole moment, Mulliken population analysis, and linear optical absorption spectrum of the system. We also demonstrate how the program can be used to compute the total energy per unit cell of a polymer. The applications presented in this paper include small organic and inorganic molecules, fullerene C 60, and model polymeric systems, viz., chains containing alternating boron and nitrogen atoms (BN chain), and carbon atoms (C chain). Program summary Program title: cindo.x Catalogue identifier: AECN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AECN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 23 304 No. of bytes in distributed program, including test data, etc.: 217 035 Distribution format: tar.gz Programming language: Fortran 90 Computer: PC's/Linux, Program has been tested with Intel Fortran Compiler (noncommercial version 10.1) and gfortran compiler (gcc version 4.3.0) with optimization option -O Operating system: Linux, Code was developed and tested on various recent versions of Fedora including Fedora 9 (kernel version 2.6.25-14) Classification: 16.1 External routines: This program needs to link with LAPACK/BLAS libraries compiled with the same compiler as the program. For the Intel Fortran Compiler we used the ACML library version 3.6.0, while for gfortran compiler we used the libraries supplied with the Fedora distribution. Nature of problem: A good starting description of the electronic structure of extended many-electron systems such as molecules, clusters, and polymers, can be obtained using the Hartree–Fock (HF) method. Solution of HF equations within a fully ab initio formalism for large systems, however, is computationally quite expensive. For such systems, semi-empirical methods such as CNDO and INDO proposed by Pople and collaborators are quite attractive. The present program can solve the HF equations for both open- and closed-shell systems containing first- and second-row atoms using either the INDO model or the CNDO model. Solution method: The single-particle HF orbitals are expressed as linear combinations of the Slater-type orbital (STO) basis set specified by Pople and coworkers. Then using the parameters prescribed for the CNDO/INDO methods, the HF integro-differential equations are transformed into a matrix eigenvalue problem. Thereby, its solutions are obtained in a self-consistent manner, using methods of computational linear algebra. Running time: Each of the examples provided takes only a few seconds to run. For a large molecule or a cluster, however, the run time may be a few minutes.

Fluorescent characteristics of coumarin photosensitizers

We present a theoretical and experimental study of the fluorescent ability of new coumarin sensitizers. Using the INDO method, we have drawn the level diagram for the photophysical processes in the coumarin molecules. We have calculated the rate constants for internal conversion and intersystem crossing and the radiative rate constants. We have determined the experimental and theoretical fluorescence yields of the test compounds.

Calculations of derivatives of porphin and porphyrazine with an annulated five-membered heteroaromatic ring using a modified INDO method

Quantum-chemical calculations for series of porphin (H2P) and porphyrazine (H2PA) derivatives whose molecules contain a 3,4-annulated five-membered heteroaromatic ring of pyrrole, furan, and thiophene as well as 1,2,5-triazole, 1,2,5-oxadiazole, and 1,2,5-thiadiazole have been carried out by the AM1 and INDO/Sm methods (m means “modified parametrization”). As follows from the unrestricted Hartree-Fock AM1 calculations, the ground state energy of the a isomer is lower than that of the b isomers for all compounds, the a and b isomers being NH isomers with the additional five-membered ring fused to a pyrrolenine or pyrrole ring, respectively. Condensation of the five-membered ring for the b isomers of the H2P derivatives is shown to extend the main conjugation path from 18-membered to 21-membered cyclopolyene. However, the 18-membered cyclopolyene for the a isomers of the H2P derivatives and 16-membered cyclopolyene for both isomers of the H2PA derivatives prove to be isolated from the five-membered ring carrying six π-electrons. Based on INDO/Sm computations of electronic absorption spectra of the H2P and H2PA derivatives, it is shown that the Qx level of the a isomers is sensitive to the nature of the annulated ring whereas the Qy level is practically not shifted. On the contrary, the Qx level of the b isomers is relatively insensitive to the nature of the annulated ring while the Qy level decreases monotonously in the H2P and H2PA series, being the first excited state level for the majority of the derivatives (X is along the NH-HN axis; Y, perpendicular to it). The electronic absorption spectra at the border of the visible and near-UV regions are determined mainly by two high-intensity G → Bx and G → By transitions for the H2P derivatives. However, four intense G → Bx, G → By, G → Nx, and G → Ny transitions are characteristic of the spectra of the H2PA derivatives.

2,6-Diphenylpyridine-based organic emitter for electroluminescent device

2,6-Diphenylpyridine-based compound ( 6) was synthesized and fully characterized. The crystal structure of 6 was determined by single crystal X-ray diffraction determination. It is fluorescent in the blue–green region. The HOMO and LUMO energy levels obtained from electrochemical and UV–vis spectrum are −5.25 and −2.48 eV, respectively. INDO method in the ZINDO program was employed to study their electron density distribution. Using the dye as light-emitting layer without doping, organic light-emitting diodes showed appropriate green emission at λ max = 518 nm. The device shows good performance with a low turn-on voltage of 3.10 V and a maximum brightness of 28,839 cd/m 2 at 14.71 V. The CIE coordinates calculated based on the EL data are (0.28, 0.58) close to the chromaticity coordinates of the NTSC standard green ( x = 0.22, y = 0.71).

Charge transport parameters of HBC at different temperatures

AbstractWe study the dependence on temperature of the charge transport parameters for hexabenzocoronene (HBC). Following from Marcus theory, two charge transport parameters will be calculated: the transfer integral and the difference in site energies. These parameters are strongly dependent on the orientation and position of molecules. Position and orientation of molecules are determined using molecular dynamics. Transfer integrals are calculated from a simplified INDO method. A technique to compute energetic disorder, that is the spread in site energies for the charge carriers, is developed. In the herringbone phase transfer integrals are higher, but so is energetic disorder. We consider three derivatives of HBC with different side chains, which lead to different phase behaviour and distributions of charge transport parameters. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Semi‐Empirical and DFT Studies on Structures and Spectra for C78(CH2)2

AbstractEighteen possible isomers of C78(CH2)2 were investigated by the INDO method. It was indicated that the most stable isomer was 42,43,62,63‐C78(CH2)2, where the –CH2 groups were added to the 6/6 bonds located at the same hexagon passed by the longest axis of C78 (C2v), to form cyclopropane structures. Based on the most stable four geometries of C78(CH2)2 optimized at B3LYP/3‐21G level, the first absorptions in the electronic spectra calculated with the INDO/CIS method and the IR frequencies of the C–C bonds on the carbon cage computed using the AM1 method were blue‐shifted compared with those of C78 (C2v) because of the bigger LUMO‐HOMO energy gap and the less conjugated carbon cage after the addition. The chemical shifts of 13C NMR for the carbon atoms on the added bonds calculated at B3LYP/3‐21G level were moved upfield thanks to the conversion from sp2‐C to sp3‐C.

UV and IR Studies on Heterofullerene C76BN

Twenty-two possible isomers for C76BN were studied by INDO methods. The two most stable geometries are 52,53-C76BN and 29,28-C76BN, in which boron and nitrogen atoms are connected with each other and located at the 6/6 bond near the longest axis of C78(C2v). Electronic spectra of C76BN were investigated with INDO/SCI method. UV absorptions of C76BN are red-shifted compared with those of C78(C2v). The structures and IR spectra for the four stable isomers of C76BN were calculated by AM1 method. It was indicated that the substitution of the BN unit weakens the conjugation of carbon atoms, leading to the decrease of IR frequencies.

Electronic Structures and Spectra of Isomers for C78O

The semi-empirical INDO method was used to study the electronic structures and the spectra of all of the 34 possible isomers of C78O based on C78 with group C2v. This calculation can simulate positions of an additional oxygen atom in C78 and predict the spectroscopic characteristics of the isomers. The most stable geometry of C78O is the 73,78-C78O molecule with an epoxide structure. The added 73,78-bond is located between two hexagons (66) and is intersected by the shortest C2 axis in C78 with group C2v. Atomic orbitals of the oxygen atom play an important role in lowering HOMO energy of 73,78-C78O. Compared with C78 with group C2v, the blue-shift in the electronic absorption spectrum for 73,78-C78O was observed. The reason of the blue-shift effect was discussed, and the electronic transitions were assigned based on the theoretical calculations.

INDO/SCF-CI calculations and structural spectroscopic studies of some complexes of 4-hydroxyacetanilide

The electronic energies among different possible structures of 4-hydroxyacetanilide (paracetamol) (PA) molecule, were calculated using INDO method and it has been concluded that its structure has C s point group symmetry of the cis-form. The ionization potential, electron affinity, dipole moment and binding energy have been calculated. The calculated electronic transitions of the cis-form of PA using SCF-CI method have good coincidence with the electronic absorption spectrum. The temperature effect on the electronic spectrum of PA confirms the presence of one conformer only. The electronic spectra of PA compound were studied in different polar- and non-polar solvents and the hydrogen bonding as well as the orientation energies of the polar solvents were determined from the mixed solvents studies. Complexes of PA with various metal ions such as, Cu(II), Zn(II) or Fe(II) ions of ratio 2:1, respectively, have been prepared and their structure has been confirmed by elemental analysis, atomic absorption spectra, IR spectra and 1H NMR spectra and finally it can be concluded that the structure of the complexes has C 2h point group symmetry in which two PA molecules are chelated to any one of the metal ions, Cu(II), Zn(II) and Fe(II) ions.