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Synthesis, structural and computational characterization of 2-amino-3,5-diiodobenzoic acid and 2-amino-3,5-dibromobenzoic acid
... Figure 4indicate the distributions and energy levels of the orbitals computed from the total energies via Koopman's theorem at the B3LYP/6-311G(d,p) basis set (Table 6). The gap between HOMO and LUMO defines the molecular chemical stability [41][42][43]. The energy values of HOMO are computed -5.9308, -5.9294, -5.9283, -5.9259, -5.8875 and -5.8018 eV and LUMO are -2.1244, ...
This study covers the synthesis, structural characterization by experimental FT-IR, ¹H-NMR and ¹³C-NMR, UV–Vis and single crystal XRD and comparison with theoretical calculations of a Schiff base compound bearing phenoxy group, C34H28N2O4 by using the DFT method 6-311G(d,p) basis set. The molecular geometry, the dipole moments, electrostatic potential, vibrational frequencies, HOMO-LUMO energy were calculated. NBO, NLO, thermodynamic properties and Fukui function were studied. In this work, theoretical values show good agreement with experimental values.
Nur Bektaş orcid.org/0000-0003-0427-225X Zeynep Demircioğlu orcid.org/0000-0001-9538-9140 Çiğdem Albayrak Kaştaş orcid.org/0000-0003-0235-7460 Orhan Büyükgüngör orcid.org/0000-0001-7133-1841 imine or azomethine group. o-hydroxy Schiff bases can exist in two tautomeric form as enol and keto forms in the solid state (Özek et al. 2007). Schiff bases are used as pigments and dyes, catalysts, intermediates in organic synthesis, and as polymer stabilisers. Schiff bases have also been shown to exhibit a broad range of biological activities, including antifungal, antibacterial, antimalarial, antiproliferative, anti-inflammatory, antiviral, and antipyretic properties (Dhar and Taploo 1982).
Detailed infrared spectrum in gas phase, NMR spectra analyses and theoretical studies of 2-amino-3-methylbenzoic acid were performed with DFT/B3LYP/6-311G+(2d,p) level of method in Gaussian 09W. Ground state molecular geometries of monomeric and dimeric structures were calculated in vacuum and compared to the experimental XRD results. Potential energy surface graphics of the proton transfer and torsional tautomerism process were obtained. Also, HOMA aromaticity chancing graphics were drowned in mentioned process. The IR band assignments and the decompositions of potential energy for each band were done using theoretical calculations. 1H and 13C NMR chemical shifts analyses were performed by using GIAO NMR calculations with SCRF solvent model.
The Schiff base compound 3,3-(1,4-phenylimino)-bis-[1,3-bis-(4-methoxyphenyl) propan-1-one)], formulated as C40H36N2O6, and its Cu(II) complex were synthesized and characterized by analytical analysis, various spectral techniques such as FT-IR, NMR, UV–vis, magnetic measurements and molar conductivity. Thermo gravimetric analysis (TGA and DTA) carried out to obtain information about its thermal stability. The molecular structure and spectroscopic properties of the ligand were obtained with FT-IR, 1H and 13C NMR, UV–vis investigations as experimentally and compared with theoretical results obtained from DFT/B3LYP/6-311þ þG(d,p) basis set. In addition to molecular calculations of the title compound, molecular electrostatic potential (MEP), dipole moments, atomic charges, HOMO–LUMO, NLO and NBO analysis were computed. The calculated results show that the optimized geometry can well reproduce the crystal structure parameters, and the theoretical vibrational frequencies, 1H and 13C NMR chemical shifts show good agreement with experimental values. Photoluminescence properties of the ligand and its Cu(II) complex were examined.
C7H6BrNO2, monoclinic, P12(1)/n1 (no. 14), a = 12.0600(6) angstrom, b = 3.9089(2) angstrom, c = 15.9816(7) angstrom, beta = 90.836(4)degrees, V = 753.3 angstrom(3), z = 4, R-gt(F)= 0.022, wR(ref)(F-2) = 0.052, T = 173 K.
The 4-((E)-(2-((E)-2, 4-dihydroxybenzylideneamino) ethylimino) methyl) benzene-1,3-diol tetradentate ligand, H2L, reacted with PdCl2 to produce the related complex. The complex was characterized by elemental analysis, infrared and electronic spectroscopy, thermogravimetric study, and molar conductance. Furthermore, the fully optimized geometries were calculated using the ADF 2009.01 package. Comparison between the calculated and experimental results covering molecular structures, assignment of fundamental vibrational modes, and thermodynamic properties were investigated. The optimized molecular geometries were compared with the experimental data obtained from X-ray data of a similar complex, which indicated that the theoretical results agree with the corresponding experimental values. The UV-Vis spectrum of the compound was also recorded and some properties, such as HOMO and LUMO energies and lambda(max), were determined using DFT (PW91) method. The absorption wavelengths were compared with the experimental data.
We have carried out a natural bond orbital analysis of hydrogen bonding in the water dimer for the near-Hartree–Fock wave function of Popkie, Kistenmacher, and Clementi, extending previous studies based on smaller basis sets and less realistic geometry. We find that interactions which may properly be described as ‘‘charge transfer’’ (particularly the n-σ*OH interaction along the H-bond axis) play a critical role in the formation of the hydrogen bond, and without these interactions the water dimer would be 3–5 kcal/mol repulsive at the observed equilibrium distance. We discuss this result in relationship to Klemperer’s general picture of the bonding in van der Waals molecules, and to previous theoretical analyses of hydrogen bonding by the method of Kitaura and Morokuma.
A method of 'natural population analysis' has been developed to calculate atomic charges and orbital populations of molecular wave functions in general atomic orbital basis sets. The natural analysis is an alternative to conventional Mulliken population analysis, and seems to exhibit improved numerical stability and to better describe the electron distribution in compounds of high ionic character, such as those containing metal atoms. An ab initio calculation is conducted of SCF-MO wave functions for compounds of type CH3X and LiX (X = F, OH, NH2, CH3, BH2, BeH, Li, H) in a variety of basis sets to illustrate the generality of the method, and to compare the natural populations with results of Mulliken analysis, density integration, and empirical measures of ionic character. Natural populations are found to give a satisfactory description of these molecules, providing a unified treatment of covalent and extreme ionic limits at modest computational cost.
The influence of amino group position towards the carboxylic group on the vibration structure of the molecule was estimated. The calculated parameters were compared to experimental characteristic of these molecules. FT-IR, FT-Raman and NMR spectra of the title compounds were recorded and analyzed. The most important vibration bands due to amino and carboxyl groups and the benzene ring were assigned. Wavenumbers and intensities for the three studied acids were compared and discussed in terms of location of the carboxylic group. A linear correlation between proton and carbon GIAO NMR shieldings of studied compounds and experimental data was found.
The results of a single-crystal structure determination when in CIF format can now be validated routinely by automatic procedures. In this way, many errors in published papers can be avoided. The validation software generates a set of evi detailing issues to be addressed by the experimenter, author, referee and publication journal. Validation was pioneered by the IUCr journal Acta Crystallographica Section C and is currently standard procedure for structures submitted for publication in all IUCr journals. The implementation of validation procedures by other journals is in progress. This paper describes the concepts of validation and the classes of checks that are carried out by the program PLATON as part of the IUCr checkCIF facility. PLATON validation can be run at any stage of the structure re®nement, independent of the structure determination package used, and is recommended for use as a routine tool during or at least at the completion of every structure determination. Two examples are discussed where proper validation procedures could have avoided the publication of incorrect structures that had serious consequences for the chemistry involved.
We present a series of calculations designed to identify an economical basis set for geometry optimizations and partial charge calculations on medium-size molecules, including neutrals, cations, and anions, with special emphasis on functional groups that are important for biomolecules and drug design. A new combination of valence basis functions and polarization functions, called the MIDI! basis set, is identified as a good compromise of speed and accuracy, yielding excellent geometries and charge balances at a cost that is as affordable as possible for large molecules. The basis set is optimized for molecules containing H, C, N, O, F, P, S, and Cl. Although much smaller than the popular 6-31G* basis set, in direct comparisons it yields more accurate geometries and charges as judged by comparison to MP2/cc-pVDZ calculations.
One of the most important steps in a Kohn-Sham (KS) type density functional theory calculation is the construction of the
matrix of the KS operator (the “Fock” matrix). It is desirable to develop an algorithm for this step that scales linearly
with system size. We discuss attempts to achieve linear scaling for the calculation of the matrix elements of the exchange-correlation
and Coulomb potentials within a particular implementation (the Amsterdam density functional, ADF, code) of the KS method.
In the ADF scheme the matrix elements are completely determined by 3D numerical integration, the value of the potentials in
each grid point being determined with the help of an auxiliary function representation of the electronic density. Nearly linear
scaling for building the total Fock matrix is demonstrated for systems of intermediate size (in the order of 1000 atoms).
For larger systems further development is desirable for the treatment of the Coulomb potential.
The method of natural localized molecular orbitals (NLMOs) is presented as a novel and efficient technique for obtaining LMOs for SCF and CI wave functions. It is an extension of the previously developed natural atomic orbital (NAO) and natural bond orbital (NBO) methods, and uses only the information contained in the one‐particle density matrix. Results are presented for methane and cytosine to indicate that NLMOs closely resemble LMOs obtained by the Boys and Edmiston–Ruedenberg methods, with the exception that the NLMO procedure automatically preserves the MO σ–π separation in planar molecules. The computation time is modest, generally only a small fraction of the SCF computation time. In addition, the derivation of NLMOs from NBOs gives direct insight into the nature of the LMO ‘‘delocalization tails,’’ thus enhancing the role of LMOs as a bridge between chemical intuition and molecular wave functions.
From the information contained in the (exact or approximate) first-order density matrix, we describe a method for extracting a unique set of atomic hybrids and bond orbitals for a given molecule, thereby constructing its "Lewis structure" in an a priori manner. These natural hybrids are optimal in a certain sense, are efficiently computed, and seem to agree well with chemical intuition (as summarized, for example, in Bent's Rule) and with hybrids obtained by other procedures. Using simple INDO-SCF-MO wave functions, we give applications of the natural hybrid orbital analysis to molecules exhibiting a variety of bonding features, including lone pairs, multiple bonds, strained rings, and "bent bonds", multiple resonance structures, hydrogen bonds, and three-center bonds. Three examples are described in greater detail: (i) "orbital following" during ammonia umbrella inversion, (ii) the dimerization of water molecules, and (iii) the hydrogen-bridged bonds of diborane.
Cited By (since 1996): 6085, Export Date: 25 August 2011, Source: Scopus
In this work, the molecular conformation, vibrational and electronic transition analysis of 2-amino-5-bromobenzoic acid (2A5BrBA) were presented for the ground state using experimental techniques (FT-IR, FT-Raman and UV) and density functional theory (DFT) employing B3LYP exchange correlation with the 6-311++G(d,p) basis set. FT-IR and FT-Raman spectra were recorded in the regions of 400-4000 cm(-1) and 50-4000 cm(-1), respectively. There are four conformers, C1, C2, C3 and C4 for this molecule. The geometrical parameters, energies and wavenumbers have been obtained for all four conformers. The computational results diagnose the most stable conformer of 2A5BrBA as the C1 form. The complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. Raman activities calculated by DFT method have been converted to the corresponding Raman intensities using Raman scattering theory. The UV spectra of investigated compound were recorded in the region of 200-400 nm for ethanol and water solutions. The electronic properties were evaluated with help of time-dependent DFT (TD-DFT) theoretically and results were compared with experimental observations. The thermodynamic properties of the studied compound at different temperatures were calculated, revealing the correlations between standard heat capacity, standard entropy, standard enthalpy changes and temperatures. The observed and the calculated geometric parameters, vibrational wavenumbers and electronic transitions were compared with observed data and found to be in good agreement.
The WinGX suite provides a complete set of programs for the treatment of small‐molecule single‐crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray‐traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.
In the present work, molecular geometry and anharmonic vibrational spectra of o-, m-, p-iodonitrobenzene have been studied. The anharmonic frequencies were calculated using second order perturbative (PT2) approach with basis set 3-21G∗ on iodine and 6-311G(d,p) on other atoms at DFT(B3LYP) level of theory and were compared to experimental values. The assignments of vibrational modes of isomeric iodonitrobenzenes were done by using potential energy distribution (PED) and vibrational assignments of benzene, nitrobenzene and iodobenzene. The combination and overtone bands are also assigned. The electronic spectra were recorded as well as simulated using polarizable continuum model (PCM) at TD-B3LYP/6-311G(d,p)/3-21G∗ level of theory. The vibrational and electronic spectra are interpreted. Moreover, atomic charges, MEP mapping, HOMO–LUMO, NBO analysis and various thermodynamics and molecular properties are reported.
The Schiff base compound (E)-1-(5-nitrothiophen-2-yl)-N-[4-(trifluoromethyl)phenyl] methanimine has been synthesized and characterized by IR, UV-Vis, and X-ray single-crystal determination. The molecular geometry from X-ray experiment in the ground state has been compared using the density functional theory (DFT) with the 6-311++G(d,p) basis set. The calculated results show that the DFT can well reproduce the structure of the title compound. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement is determined with the experimental ones. The nonlinear optical properties are also addressed theoretically. In addition, DFT calculations of the title compound, molecular electrostatic potential (MEP), and thermodynamic properties were performed at B3LYP/6-311++G(d,p) level of theory. (c) 2013 Elsevier B.V. All rights reserved.
The vibrational (FT-IR and FT-Raman) and NMR ( and ) spectra of Ca, Mn, and Zn complexes with ortho-, meta-, and para-iodobenzoic acids have been studied. The solid state samples of all complexes have been measured within the range 4000–400 cm−1, while water solutions of ortho-iodobenzoates within the range 4000–800 cm−1. Based on previous experimental data and normal mode calculations for simpler complexes the assignment of bands observed in vibrational spectra of studied compounds has been done. Some significant differences in vibrational structure (frequency and intensity of selected bands) have been observed and discussed. The effect of metal on ring vibrations and carboxylic anion stretching and deformation has been investigated. Also, influence of iodine substitution on the aromatic ring and carboxylic anion, depending on iodine ring position, has been discussed. In case of soluble compounds, wavenumbers of characteristic bands of water solution samples have been compared with wavenumbers of corresponding bands of solid state samples.
In this study, molecular geometries, experimental vibrational wavenumbers, electronic properties and quantum chemical calculations of 2-thiopheneglyoxylic acid molecule, (C6H4O3S), and its metal halides (Cd, Co, Cu, Ni and Zn) which are used as pharmacologic agents have been investigated experimentally by FT-IR, micro-Raman and UV-visible spectroscopies and elemental analysis. Meanwhile the vibrational calculations were verified by DFT/B3LYP method with 6-311++G(d,p) and LANL2DZ basis sets in the ground state, for free TPGA molecule and its metal halide complexes, respectively, for the first time. The calculated fundamental vibrational frequencies for the title compounds are in a good agreement with the experimental data.
The antioxidative properties of syringic, 3,4-dihydroxybenzoic, sinapic and caffeic acids were studied in the concentration range 0.002–0.02% (0.9×10−4–1.3×10−3 M) during autoxidation of triacylglycerols of sunflower oil at 22 and at 90 °C. The stabilization factor (F) as a measure of effectiveness, the oxidation rate ratio (ORR) as a measure of strength, and the activity (A) which combines the above two factors were determined. The effectiveness of the phenolic acids increased in the following order: syringic acid
The crystallographic problem: The production, and the visibility in the published literature, of thermal ellipsoid plots for small-molecule crystallographic studies remains an important method for assessing the quality of reported results. Since the mid 1960s, the program ORTEP (Johnson, 1965) has been perhaps the most popular computer program for generating thermal ellipsoid drawings for publication. The recently released update of ORTEP-III (Johnson & Burnett, 1996) has some additional features over the earlier versions, but still relies on fixed-format input files. Many users will find this very inconvenient, and will prefer to obtain drawings directly from their crystallographic coordinate files. This new version of ORTEP-3 for Windows provides all the facilities of ORTEP-III, but with a modern Graphical User Interface (GUI). Method of solution: A Microsoft-Windows GUI has been added to ORTEP-III. All the facilities of ORTEP-III are retained, and a number of extra features have been added. The GUI is effectively an editor that writes ORTEP-III input files, but the user need not have any knowledge of the inner workings of ORTEP. The main features of this program are: (i) ORTEP-3 for Windows can directly read many of the common crystallographic ASCII file formats. Currently supported formats are SHELX (Sheldrick, 1993), GX (Mallinson & Muir, 1985), GIF (Hall, Allen & Brown, 1991), SPF (Spek, 1990), CRYSTALS (Watkin, Prout, Carruthers & Betteridge, 1996), CSD-XR and CSD-FDAT. In addition, ORTEP-3 for Windows will accept any legal ORTEP-III instruction file. (ii) Covalent radii for the first 94 elements are stored internally, and may be modified by the user. All bonds are calculated automatically, and any individual bonds may be selected for removal, or for a special representation. (iii) The graphical representations of thermal ellipsoids for any element or selected sets of atoms can be individually set. All the possible graphical representations of thermal ellipsoids in ORTEP-III are also available in ORTEP-3 for Windows. (iv) A mouse labelling routine is provided by the GUI. Any number of selected atoms may be labelled, and any available Windows font may be used for the labels. The font attributes, e.g. italic, bold, colour, point size etc. can also be selected via a standard Windows dialog box. (v) As well as HPGL and PostScript Graphics graphic metafiles, it is also possible to get high quality graphics output by printing directly to an attached printer. The screen display may be saved as BMP or PCX format metafiles, and may also be copied to the clip-board for subsequent use by other Windows programs, e.g. word processing or graphics processing programs. Colour is available for all these output modes. (vi) A simple text editor is provided, so that input files may be modified without leaving the program. (vii) Symmetry expansion of the asymmetric unit to give complete connected fragments may be carried out automatically. (viii) Unit-cell packing diagrams are produced automatically. (ix) A number of options are provided to control the view direction. The molecular view may be rotated or translated by button commands from the tool bar, and views normal to crystallographic planes may also be obtained. Software environment and program specification: The program will read several common crystallographic file formats which hold information on the anisotropic displacement parameters. The operation of the program is carried out via standard self-explanatory MS-Windows menu items and dialog boxes. Hard-copy output is either by HPGL or Encapsulated PostScript metafiles, or by directly printing the graphics screen. Hardware environment: The program is implemented for IBM PC compatible computers running MS-Windows versions 3.1x, Windows 95 or Windows NT. At least a 486-66 machine is recommended with 8 Mbytes of RAM, and at least 5 Mbytes of disk space. Documentation and availability: The executable program, together with full documentation, is available free for academic users from http://www.chem. gla.ac.uk/̃louis/ortep3. Although the program is written in Fortran77, a large number of nonstandard FTN77 calls are used to create the GUI. For this reason, the source code is not available.
The crystal structures of ammonium and sodium 2-amino-3,5-dichlorobenzoates were determined by the X-ray diffraction method. The ammonium salt crystallizes in the monoclinic system (space group P21/c) with a = 13.941(3), b = 9.128(3), c = 7.349(2) Å, β = 90.80(3)° and Z = 4. The structure consists of an ammonium cation hydrogen bonded to a carboxylate oxygen of the 2-amino-3,5-dichlorobenzoate anion. The sodium salt of 2-amino-3,5-dichlorobenzoic acid crystallizes in the triclinic system (space group P1) with a = 8.033(2), 6 = 8.944(2), c = 17.350(3) Å, α = 76.72(3)°, β = 79.69(3)°, γ = 72.54(3)° and Z = 4. The compound is a polymer in which the sodium ions are coordinated by carboxylate oxygen atoms of the organic ligand and water molecules in an octahedral arrangement. IR spectra of the salts are discussed.
Effect of solvents, buffer solutions of different pH and β-cyclodextrin (β-CD) on the absorption and fluorescence spectra of 2-aminobenzoic acid (2ABA) have been investigated. The inclusion complex of 2ABA with β-CD is discussed by semiempirical quantum calculations (AM1), absorption, emission, FT-IR, 1H NMR and scanning electron microscope (SEM). The Stokes shifts in 2ABA is correlated with different polarity scales suggest that 2ABA molecule is more polar in the S1 state. The increase in the excited state dipole moment values and β-CD studies confirm that the presence of intramolecular charge transfer (ICT) in 2ABA. Acidity constants for different prototropic equilibria of 2ABA in the S0 and S1 states are calculated. β-CD studies shows that (i) at pH∼1, 2ABA forms 1:1 inclusion complex with β-CD, whereas at pH∼7, it forms mixture of 1:1 and 1:2 inclusion complex and (ii) at pH∼1, appearance of dual luminescence in higher β-CD solutions indicates carboxyl and amino groups present in the hydrophobic part of the β-CD. A mechanism is proposed to explain the inclusion process.
The assignment of the vibrational spectra of p-halogenobenzoic acid complexes with Mg, Ca, Sr and Ba is proposed. The influence of the metals on the electronic system of p-halogenobenzoic acids is the topic of study. The biggest differences in wavenumber of selected bands dependent on metal ion occurred within the spectral range: 1604–1612, 1550–1520, 1440–1410, 1302–1243, 1100–1090 and 875–865cm−1. The influence of halogen (F, Cl, Br and I) on the electronic system of complexes was also investigated. The effect of halogen was mostly seen within the spectral range: 1610–1580, 1546–1540, 1183–1164, 1019–849 and 688–681cm−1. The main factor responsible for the changes in the vibrational structure of the molecules was the ionic potential.
The infrared spectra of 1,2,3-; 1,2,4- and 1,3,5-trimethylbenzenes have been recorded in the liquid phase in the region 250–4000 cm on a Perkin Elmer Grating Spectrophotometer model 521. Under the general symmetry considerations, the molecule 1,2,4-belongs to C2v point group, the 1,2,3-isomer belongs to Cs and the 1,3,5-isomer to D3h point group. The observed bands have been assigned to different modes of vibrations.
We report accurate ab initio studies of the first static hyperpolarizabilities (β) of fluorenyl derivatives in which electron donating (D) and electron accepting (A) groups were introduced either side of the fluorenyl ring system. Geometries of all molecules were optimized at the Hartree–Fock level in a series of steps, first with the STO-3G minimal basis set, then with the 3-21G split valence basis set and finally with the 6-31G basis set. The first static hyperpolarizabilities of these molecules were calculated using Hartree–Fock level using 6-31G basis set using gaussian98W. The calculated hyperpolarizabilities of these molecules were compared with biphenyl derivatives and other available data in the literature. To understand this phenomenon in the context of molecular orbital picture, we examined the molecular HOMOs and molecular LUMOs generated via gaussian98W. The study reveals that the fluorenyl derivatives have large β values hence in general may have potential applications in the development of non-linear optical materials.
The potential interest of vanillin, isovanillin, thiovanillin, and isothiovanillin as starting units for the design of hyperpolarizable molecules such as polyenovanillin (Ar-(CP double bond CH)(n)-CH double bond O) and bisvanillin derivatives was investigated by a CNDO/S method using a specific program that allowed the calculation of all the components of the first-order molecular hyperpolarizability tenser beta in nonpolar solvents. The reliability of the calculations was assessed by comparison with EFISH measurements on model systems. Among the vanillin derivatives, thiovanillin, where the sulfur group is in para to the aldehyde group, showed the largest hyperpolarizability, beta. In polyenovanillins, the magnitude of beta was predicted to increase as m(2) (m being the number of unsaturated bonds between the donor substituents of the aromatic ring and the aldehyde group), without saturation effect on the hyperpolarizability density p = beta/V at least up to m = 9. The calculations indicated that the thiovanillyl group (and its S-alkylated derivatives) was equivalent to the p-(dimethylamino)phenyl group in its ability to enhance the hyperpolarizability of polyenic systems, a result which may have important practical consequences. In bisvanillin, for torsion angles between the benzene rings greater than 25 degrees, the magnitude of beta was calculated to be the vector addition of the contributions of the monomer units, while for smaller angles, approaching planarity (in the cisoid conformation), a significant enhancement due to the conjugation of the two benzene rings was evidenced. It was concluded from this analysis that polyenovanillin and bisvanillin derivatives represent an interesting new family of hyperpolarizable molecules for applications in nonlinear optics.
The intramolecular thione-thiol tautomerism and intermolecular double proton transfer reaction of the hydrogen-bonded thione and thiol dimers in the title triazole compound were studied at the B3LYP level of theory using 6−311++G(d,p) basis function. The influence of the solvent on the single and double proton transfer reactions was examined in three solvents (chloroform, methanol and water) using the polarizable continuum model (PCM) approximation. The computational results show that the thione tautomer is the most stable isomer with a very high tautomeric energy barrier both in the gas phase and in solution phase, indicating a quite disfavored process. The solvent effect is found to be sizable with increasing polarity. In the double proton transfer reaction, the thione dimer is found to be more stable than thiol dimer both in the gas phase and in solution phase. The energetic and thermodynamic parameters of the double proton transfer process show that the double proton exchange from thione dimer to thiol dimer is thermodynamically unfavored. However, the exchange from thiol dimer to thione dimer for the gas phase and water phase seems to be feasible with a low barrier height and with a negative value in enthalpy and free energy changes. In addition, the hydrogen bonding interactions were analyzed in the gas phase regarding their geometries and energies. It is found that all complex formations are enthalpically favored, and the stability of the H-bonds comes in the order of S1—H2···N2 > N2—H2···S1 > N3—H3B···O1. Finally, non-linear optical properties were carried out at the same calculation level in the gas phase.
Figure
The mechanisms of the single and double proton transfer processes.
Fukui functions (softnesses) are calculated for three species - formaldehyde, the thiocyanate ion and carbon monoxide. The fukui function for a molecule has been defined as the derivative of electron density with respect to the change of number of electrons, keeping the positions of nuclei unchanged; this differentiation is performed by finite difference. Local softness and fukui function are proportional. The calculated results, expressed in terms of contour maps and condensed values of fukui functions, substantiate the previous argument that fukui functions serve as reactivity indices for chemical reactions. Particularly, it is confirmed that: (1) a nucleophilic reagent approaches the carbon atom in formaldehyde from the direction perpendicular to the molecular plane, while an electrophilic reagent approaches the oxygen atom in the molecular plane; (2) the sulphur end is softer than the nitrogen end in the thiocyanate ion; and (3) carbon monoxide behaves like a Lewis acid in bonding with transition metals.
Two antipyrine derivates, both with formula C18H15Cl2N3O, are structurally similar Schiff bases derived from the condensation of 2,3-dichlorobenzaldehyde or 2,5-dichlorbenzaldehyde with 4-aminoantipyrine in methanol solution. The compounds were characterized by elemental analysis, FT-IR, FT-Raman, UV–vis and X-ray single crystal diffraction techniques. As expected, both compounds adopt trans configurations about the Schiff base imine CN bonds. Density functional calculations were performed to further optimize and characterize them. The results indicate that the theoretical values show good agreement with experimental ones. The thermodynamic functions (standard heat capacities, standard entropies and standard enthalpy changes) and their correlations with temperatures have been obtained from their theoretical harmonic frequencies of the optimized structures. The intramolecular electronic transfer and nonlinear optical properties of the compounds can be explained clearly by the molecular frontier orbitals and pi-electron systems.
We present the theoretical and technical foundations of the Amsterdam Density Functional (ADF) program with a survey of the characteristics of the code (numerical integration, density fitting for the Coulomb potential, and STO basis functions). Recent developments enhance the efficiency of ADF (e.g., parallelization, near order-N scaling, QM/MM) and its functionality (e.g., NMR chemical shifts, COSMO solvent effects, ZORA relativistic method, excitation energies, frequency-dependent (hyper)polarizabilities, atomic VDD charges). In the Applications section we discuss the physical model of the electronic structure and the chemical bond, i.e., the Kohn–Sham molecular orbital (MO) theory, and illustrate the power of the Kohn–Sham MO model in conjunction with the ADF-typical fragment approach to quantitatively understand and predict chemical phenomena. We review the “Activation-strain TS interaction” (ATS) model of chemical reactivity as a conceptual framework for understanding how activation barriers of various types of (competing) reaction mechanisms arise and how they may be controlled, for example, in organic chemistry or homogeneous catalysis. Finally, we include a brief discussion of exemplary applications in the field of biochemistry (structure and bonding of DNA) and of time-dependent density functional theory (TDDFT) to indicate how this development further reinforces the ADF tools for the analysis of chemical phenomena. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 931–967, 2001
A variety of atomic and molecular properties can be expressed in terms of the electrostatic potential. These include energies,
covalent and anionic radii, electronegativities (chemical potentials) and a variety of properties that depend upon noncovalent
interactons. We present a survey of such relationships, which may be exact or approximate; they may involve the potential
in three-dimensional space, along the axes between bonded atoms, at nuclei or on molecular surfaces. Thus, the electrostatic
potential, which is rigorously related to the electronic density by Poisson's equation, can be regarded as, effectively, another
fundamental determinant of atomic and molecular properties.
Escherichia coli incubated with subinhibitory concentrations of p-aminobenzoic acid at pH 5.5 produced either larger or more opaque cells than the control culture. DNA synthesis was particularly sensitive to the presence of p-aminobenzoic acid. The antibacterial effect of p-aminobenzoic acid was reduced by the presence of folinic acid in the culture of Pseudomonas aeruginosa. These findings indicate that the effect of p-aminobenzoic acid on DNA synthesis may be via an action on the dihydrofolate reductase enzyme.
The single crystals of methyl p-hydroxy benzoate (MPHB) are grown from methanol solution by a low temperature solution growth technique. The SHG efficiency is tested using Q-switched Nd:YAG laser of wavelength λ at 1064 nm, which is approximately 1.2 times that of urea. Vibrational spectral analysis using NIR-FT Raman and FT-IR spectra is carried out to understand the structural and electronic contributions to hyperpolarizability in MPHB. The DFT computations are also performed at B3LYP/6-311G(d,p) level to derive equilibrium geometry, vibrational wavenumbers and intensities. The results of ab initio calculations at HF/6-311G(d,p) level show that the vibrational contribution for the second-order electro-optic coefficient in MPHB is about 19.5%. Vibrational spectral studies also provide evidence for the charge transfer interaction between the donors and the acceptor group through the π-system. The π-electron cloud movement from donor to acceptor can make the molecule highly polarized and the intramolecular charge transfer interaction must be responsible for the nonlinear optical properties of MPHB. The splitting of the carbonyl mode may be attributed to the intramolecular association based on CO⋯H type hydrogen bonding in the molecule. The conjugation and influence of intermolecular hydrogen bonding (CO⋯H) type network in the crystal results in lowered CO stretching wavenumber.
Some new biotransformation products, p-aminobenzoic acid 7-O-β-d-glucopyranosyl ester, N-acetyl p-aminobenzoic acid 7-O-β-d-glucopyranosyl ester, o-aminobenzoic acid 7-O-β-d-(β-1,6-O-d-glucopyranosyl)glucopyranosyl ester and o-aminobenzoic acid 7-O-β-d-glucopyranosyl ester were isolated from cell suspension cultures of Solanum mammosum following administration of p-aminobenzoic acid, N-acetyl p-aminobenzoic acid or o-aminobenzoic acid respectively. N-acetyl p-aminobenzoic acid and N-formyl p-aminobenzoic acid were also identified as cell suspension metabolites of p-aminobenzoic acid.
This paper is the second in a series to assign CX stretching and deformational modes in halogeno-benzenes. The assignment of these CCl and CBr modes are easily achieved by comparison of the chloro and bromo-compounds.The CN stretching frequencies of the halogeno-nitrobenzenes have been assigned in the region 1280–1240 cm−1, and these frequencies have been chosen by comparison of known CN stretching frequencies of other nitrogen compounds with the known CN bond lengths. The low frequency band at about 800 cm−1, previously assigned to the CN stretch, is now shown to be the NO2 in-plane deformation.The modification of the substitution pattern in the o-, m- and p- isomers due to the presence of a deactivating group has been considered. In the o-isomers the band at 775 cm−1 has been considered as indicative of electronic interaction between the two ortho groups.
Prompted by a recent paper by Maynard and co-workers (Maynard, A. T.; Huang, M.; Rice, W. G.; Covel, D. G. Proc. Natl. Acad. Sci. U.S.A. 1998. 95, 11578), we propose that a specific property of a chemical species. the square of its electronegativity divided by its chemical hardness, be taken as defining its electrophilicity index. We tabulate this quantity for a number of atomic and molecular species, for two different models of the energy-electron number relationships, and we show that it measures the second-order energy change of an electrophile as it is saturated with electrons.
Despite the remarkable thermochemical accuracy of Kohn–Sham density-functional theories with gradient corrections for exchange-correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact-exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange-correlation functional containing local-spin-density, gradient, and exact-exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first- and second-row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
It is demonstrated that the variation of the gas-phase basicities of amines can be analyzed by using two parameters: one global and one local (that is, site-dependent). Two global quantities (the average "effective" electronegativity and the geometric average of the isolated-atom electronegativities) and two local quantities (the fukui function and the residual charges) are tested. A two-parameter linear model containing one global and one local quantity produces satisfactory correlations with the experimental gas-phase basicities. It is shown how to express the fukui function, which reflects the site reactivity in density functional theory (f(r⇒) = [∂ρ(r→)/∂N]ν(7), in terms of the variation of the Mulliken gross charges (qi) of an atom in a molecule, which is accompanied with a change in the total number of electrons (N) in this molecule: fi+ = qi(N + 1) - qi(N); fi- = qi(N) - qi(N-1) and f1° = 1/2[qi(N + 1) - qi(N - 1)].
The Schiff base compound (E)-2-[(2-chlorophenyl)iminomethyl]-4-trifluoromethoxyphenol has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray experiment in the ground state has been compared using the density functional theory (DFT) with the 6-311++G(d,p) basis set. The calculated results show that the DFT can well reproduce the structure of the title compound. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and a good agreement is determined with the experimental ones. To investigate the tautomeric stability, optimization calculations at the B3LYP/6-311++G(d,p) level were performed for the enol and keto forms of the title compound. Calculated results reveal that its enol form is more stable than its keto form. The predicted nonlinear optical properties of the title compound are much greater than those of urea. The changes of thermodynamic properties for the formation of the title compound with the temperature ranging from 200 to 500 K have been obtained using the statistical thermodynamic method. At 298.15 K, the change of Gibbs free energy for the formation reaction of the title compound is -824.841 kJ/mol. The title compound can spontaneously be produced from the isolated monomers at room temperature. The tautomeric equilibrium constant is also computed as 3.85 × 10(-4) at 298.15 K for enol↔keto tautomerization of the title compound. In addition, a molecular electrostatic potential map of the title compound was performed using the B3LYP/6-311++G(d,p) method.
In this study, the molecular conformation, vibrational and electronic transition analysis of 2,3-difluorobenzoic acid and 2,4-difluorobenzoic acid (C7H4F2O2) were presented using experimental techniques (FT-IR, FT-Raman and UV) and quantum chemical calculations. FT-IR and FT-Raman spectra in solid state were recorded in the region 4000-400 cm(-1) and 4000-5 cm(-1), respectively. The UV absorption spectra of the compounds that dissolved in ethanol were recorded in the range of 200-800 nm. The structural properties of the molecules in the ground state were calculated using density functional theory (DFT) and second order Møller-Plesset perturbation theory (MP2) employing 6-311++G(d,p) basis set. Optimized structure of compounds was interpreted and compared with the earlier reported experimental values. The scaled vibrational wavenumbers were compared with experimental results. The complete assignments were performed on the basis of the experimental data and total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. A study on the electronic properties, such as absorption wavelength, excitation energy, dipole moment and frontier molecular orbital energy, were performed by time dependent DFT (TD-DFT) approach. Based on the UV spectra and TD-DFT calculations, the electronic structure and the assignments of the absorption bands of steady compounds were discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecules.
The electrostatic potential V(r) that is created in the space around a molecule by its nuclei and electrons (treated as static distributions of charge) is a very useful property for analyzing and predicting molecular reactive behavior. It is rigorously defined and can be determined experimentally as well as computationally. The potential has been particularly useful as an indicator of the sites or regions of a molecule to which an approaching electrophile is initially attracted, and it has also been applied successfully to the study of interactions that involve a certain optimum relative orientation of the reactants, such as between a drug and its cellular receptor. A variety of methods for calculating V(r) is available, at different levels of rigor. For large biologically active molecules, multipole expansions and superposition of potentials computed for subunits have been found to be effective. A large number of chemical and biochemical systems and processes have now been studied in terms of electrostatic potentials. Three examples of such applications are surveyed in this paper. These deal with: (a) reactive properties of nucleic acids, including their component bases; (b) biological recognition processes, including drug-receptors and enzyme-substrate interactions; and (c) chemical carcinogenesis, referring specifically to the polycyclic aromatic hydrocarbons and halogenated olefins and their epoxides. For each of these areas, examples of the use of electrostatic potentials in elucidating structure-activity patterns are given.
The m-, o- and p-isomers of aminobenzoic acid (ABA) repressed the mutagenicity of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) in Salmonella typhimurium TA100. Their antimutagenic potency was in the order of o-ABA > m-ABA > p-ABA. The mechanism of this antimutagenicity is ascribed mainly to the decomposition of MNNG induced by the aminobenzoic acid isomers outside or within the bacterial cells. The inhibition of plant cell peroxidases and bacterial acetyltransferases that are required for the plant activation of 2-aminofluorene (2-AF) to mutagenic product(s) may participate in the repression of 2-AF mutagenesis by the aminobenzoic acids in S. typhimurium strain YG1024. The aminobenzoic acid isomers exhibited no inhibitory effects towards the direct-acting agent 2-acetoxy-2-acetylaminofluorene, the stable diacetylated metabolic product of 2-AF.
This contribution explores the relation between molecular second hyperpolarizabilities (gamma) and molecular architecture in phenylacetylene dendrimers using the semiempirical molecular orbital method, that is, INDO/S method. The orientationally averaged gamma of a large-size phenylacetylene dendrimer, which is composed of 24 units of phenylacetylenes and is referred to as D25, is found to be about 50 times as large as that of the diphenylacetylene monomer. In contrast, the gamma(s)() value of D25 is found to be about 6 times as small as that of the para-substituted phenylacetylene oligomer (L25) composed of 24 units of phenylacetylenes. To investigate the structure-property relation in gamma for D25 and L25, we examine the spatial contributions of electrons to gamma values using gamma density analysis. The present analysis reveals that the dominant contributions of electrons to gamma of D25 are localized in the linear-leg regions parallel to the applied electric field and the contributions are also well segmented at the meta-connected points (benzene rings), while the spatial distribution of the gamma density of L25 is extended over the whole region of the chain, and the dominant contribution stems from the both-end regions. It is found for D25 that the magnitude of contributions to gamma in the internal region is more enhanced than that in the outer region. We further found that the magnitudes of contributions in internal linear-leg regions of D25 are somewhat larger than those of the same-size isolated linear-leg molecules. This suggests that the slightly remaining pi-conjugations via the meta-branching points still enhance the contributions to gamma localized in the linear-leg regions. These features of spatial contributions to gamma of D25 are found to originate in the fractal architecture, in which pi-conjugation lengths in the linear-leg region increase on going from the periphery to the core. Finally, fractal antenna dendrimers are expected to be promising novel nonlinear optical (NLO) substances with a controllability of the magnitude and spatial contribution of the third-order NLO properties.
We present a quantum-chemical analysis of the molecular structure and second- and third-order polarizabilities in a series of promising nonlinear optical (NLO) chromophores, the zwitterionic ammonio/borato diphenylpolyenes, R3N+Ph(C=C)nPhB-R3, whose synthesis has been reported recently. The molecular geometries are obtained via MP2/6-31G optimization, while the NLO properties are calculated with the INDO Hamiltonian using the sum-over-states and finite-field real-space methods. The real-space approach allows the direct evaluation of the NLO-active segments of the molecules, while the sum-over-states results illustrate the virtual excitations and charge-transfer pathways that are essential in the NLO response. Both methods highlight the remarkable and unexpected result that it is the strongly polarized phenylene groups that play the key role in generating a high NLO response.
FT-IR and Raman experimental data were assigned to appropriate bond vibrations and used to compare the different electronic charge distributions in the aromatic rings and carboxylic anions of various lithium, sodium, potassium, rubidium and caesium o-iodobenzoates and picolinates. Then principal component analysis (PCA) was applied in order to attempt to distinguish the biological activities of these compounds according to selected band wavenumbers. The growth of the bacteria Escherichia coli and Bacillus subtilis and the yeasts Saccharomyces cerevisiae and Hansenula anomala under optimal growth conditions were measured after 24 hours of incubation by the classical plate method. The influence of the picolinates and o-iodobenzoates on the growth of these microorganisms, again after 24 hours of incubation, was also measured and compared to the effect of sodium benzoate, which was used as a reference material. In general, the o-iodobenzoates exhibited more activity against the microorganisms than the picolinates. A statistically significant linear correlation between the spectral data and the degree of influence of a given compound on microorganism growth was established. The correlation coefficients for the o-iodobenzoates were 0.696, -0.628, 0.693 and 0.755 for E. coli, B. subtilis, H. anomala and S. cerevisiae, respectively, and for the picolinates they were 0.818, 0.826, 0.821 and 0.877 for E. coli, B. subtilis, H. anomala and S. cerevisiae, respectively. Therefore, IR spectroscopy is shown to be a rapid and reliable analytical tool for preliminary estimation of the antimicrobial properties of newly synthesized compounds, that can be applied before microbial performance tests.
The Fourier transform Raman and Fourier transform infrared spectra of 5-amino-2-chlorobenzoic acid (5A2CBA) were recorded in the solid phase. Geometry opitimizations were done without any constraint and harmonic-vibrational wavenumber and several thermodynamic parameters were calculated for the minimum energy conformer at ab initio and DFT levels invoking 6-311G(d,p) basis set and the results are compared with the experimental values with the help of three specific scaling procedures, the observed vibrational wavenumbers in FTIR and FT-Raman spectra were analyzed and assigned to different normal modes of the molecule. Most of the modes have wavenumbers in the expected range, the error obtained was in general very low. The appropriate theoretical spectrograms for the FTIR spectra of the title molecule were also constructed.