Molecular Geometry Optimization Research Articles

Using Free Computational Resources To Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted in silico drug design methods, such as molecular geometry optimization, pharmacophore modeling, protein–ligand docking simulations, homology modeling, virtual screening, and pharmacokinetics/toxicity predictions. Freely available software and web servers are selected to compose this pedagogical resource, such that it can be easily implemented in any institution equipped with an Internet connection and Windows OS computers. This material is an illustration of a drug discovery pipeline, starting from the structure of known drugs to obtain novel bioactive compounds, and, therefore, is a valid pedagogical instrument for educating future professionals in the field of drug development.

Thermodynamic properties of 1-naphthol: Mutual validation of experimental and computational results

Thermodynamic properties for 1-naphthol (Chemical Abstracts registry number [90-15-3]) in the ideal-gas state are reported based on both experimental and computational methods. Measured properties included the triple-point temperature, enthalpy of fusion, and heat capacities for the crystal and liquid phases by adiabatic calorimetry; vapor pressures by inclined-piston manometry and comparative ebulliometry; and the enthalpy of combustion of the crystal phase by oxygen bomb calorimetry. Critical properties were estimated. Entropies for the ideal-gas state were derived from the experimental studies for the temperature range 298.15⩽T/K⩽600, and independent statistical calculations were performed based on molecular geometry optimization and vibrational frequencies calculated at the B3LYP/6-31+G(d,p) level of theory. The mutual validation of the independent experimental and computed results is achieved with a scaling factor of 0.975 applied to the calculated vibrational frequencies. This same scaling factor was successfully applied in the analysis of results for other polycyclic molecules, as described in a series of recent articles by this research group. This article reports the first extension of this approach to a hydroxy-aromatic compound. All experimental results are compared with property values reported in the literature. Thermodynamic consistency between properties is used to show that several studies in the literature are erroneous. The enthalpy of combustion for 1-naphthol was also measured in this research, and excellent agreement is seen with several values already reported in the literature.

Thermodynamic properties of xanthone: Heat capacities, phase-transition properties, and thermodynamic-consistency analyses using computational results

Heat capacities and phase-transition properties for xanthone (IUPAC name 9H-xanthen-9-one and Chemical Abstracts registry number [90-47-1]) are reported for the temperature range 5<T/K<524. Statistical calculations were performed and thermodynamic properties for the ideal gas were derived based on molecular geometry optimization and vibrational frequencies calculated at the B3LYP/6-31+G(d,p) level of theory. These results are combined with sublimation pressures from the literature to allow critical evaluation of inconsistent enthalpies of sublimation for xanthone, also reported in the literature. Literature values for the enthalpy of combustion of xanthone are re-assessed, a revision is recommended for one result, and a new value for the enthalpy of formation of the ideal gas is derived. Comparisons with thermophysical properties reported in the literature are made for all other reported and derived properties, where possible.

Synthesis and properties of azonaphtharylamide pigments having arylamide groups at 2- and 7-positions

We studied two azonaphtharylamide pigments having arylamide groups at the 2- and 7-positions on the naphthol ring. Presence of the 7-substited amide group distinguishes the pigments from conventional azonaphtharylamide pigments derived from 3-hydroxy-2-naphthoic acid. The 7-substituent caused a hyperchromic effect but did not produce bathochromic shift in the optical absorption spectra in solution compared with the corresponding 7-unsubstituted counterparts. Molecular geometry optimizations through semi-empirical MO calculations showed that extent of the chromophore systems in the pigments with and without the 7-substituent is nearly the same, which is consistent with absence of the bathochromic shift. The MO calculations also showed that the MOs localized in the 7-substituents are involved in the electronic transitions in the longest wavelength bands of the pigments, which is responsible for the hyperchromic effect. The 7-substituted pigments exhibited better resistivity to light and heat than the 7-unsubstituted ones.

Density functional theory, comparative vibrational spectroscopic studies, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis of Linezolid

The Fourier transform infrared spectra and Fourier transform Raman spectra of Linezolid have been recorded in the regions 4,000–400 and 4,000–100 cm−1, respectively. Utilizing the observed Fourier transform infrared spectra and Fourier transform Raman spectra data, a complete vibrational assignment and analysis of the fundamental modes of the compound have been carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, have been calculated by density functional theory with 6-31G(d,p), 6-311G(d,p) and M06-2X/6-31G(d,p) levels. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of Linezolid is reported. Mulliken’s net charges have also been calculated. Ultraviolet–visible spectrum of the title molecule has also been calculated using time-dependent density functional method. Besides, molecular electrostatic potential, highest occupied molecular orbital and lowest unoccupied molecular orbital analysis and several thermodynamic properties have been performed by the density functional theoretical method.

The fluorescence and electronic structure of phenyl-substituted tetraazachlorin molecules

The effect of the addition of phenyl groups to pyrrole rings of tetraazachlorins, a new class of tetrapyrroles, on the photophysical properties and electronic structure of the molecules has been investigated by a complex of experimental and theoretical methods. Characteristics of fluorescence at 293 and 77 K have been determined for phenyl-substituted tetraazachlorins. The objects of this study include unsubstituted tetraazaporphine. The introduction of phenyl groups affords a marked increase in the fluorescence quantum yield. For tetraazaporphine and phenyl-substituted tetraazachlorins, fluorescence buildup occurs as the temperature is decreased from 293 to 77 K, but to a lesser extent than for tetraazachlorins having no phenyl groups, which were earlier studied by the authors. The fluorescence buildup mechanism is discussed. The singlet oxygen generation quantum yield has been determined for the tetrapyrroles examined. This characteristic increases upon tetrapyrrole is phenylation. The electronic structure and absorption spectra of unsubstituted porphine and chlorin, tetraazaporphine, tetraazachlorin, octaphenyltetraazaporphine, and tetramethylhexaphenyltetraazachlorin have been calculated by the INDO/Sm method (original modification of the INDO/S method) with molecular geometry optimization using DFT. The results of the quantum-chemical calculation of the absorption spectra are in good agreement with experimental data for transitions to the lowest excited electronic states Qx(S1) and Qy(S2).

Effect of Neighbors on the Conformational Preferences of Glycosidic Linkages in Glycyrrhizic Acid and Its Mono- and Dideprotonated Forms: X-ray, NMR, and Computational Studies

Three-dimensional structure of glycyrrhizic acid is determined by the conformation of the disaccharide unit and its relative orientation to a virtually rigid aglycone. X-ray crystallography, NMR spectroscopy, and density functional theory (DFT) calculations were used to study the conformational preferences of the glycosidic linkages in solid state, solution and vacuo, respectively. Experimental data have revealed that conformation of glycosidic bonds, that is adopted in the solid state, is also favored in solution. The molecular geometry optimizations have shown that a strongly twisted orientation of the two glucopyranose units, characteristic of the solid state, is stabilized by the bridging interaction of water molecules and/or cations with disaccharide COOH/COO¯ groups. Our results illustrate the impact of environment on the preferred conformation of disaccharide unit in the studied glycoside and point to a possible reason for the observed rigid conformation of the glycosidic bonds in solution and in t...

Spectroscopic (FTIR, FT-Raman), molecular electrostatic potential, NBO and HOMO–LUMO analysis of P-bromobenzene sulfonyl chloride based on DFT calculations

The FTIR and FT-Raman spectra of P-bromobenzene sulfonyl chloride (P-BBSC) have been recorded in the regions 4000–400cm−1 and 3500–50cm−1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method. A good agreement between experimental and calculated normal modes of vibrations has been observed. A detailed interpretation of the infrared and Raman spectra of P-BBSC is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms. The UV–vis spectral analysis of P-BBSC has also been done which confirms the charge transfer of the molecule.

Molecular structure, spectroscopic (FTIR, FT-Raman, 13C and 1H NMR, UV), polarizability and first-order hyperpolarizability, HOMO–LUMO analysis of 2,4-difluoroacetophenone

The FTIR and FT-Raman spectra of 2,4-difluoroacetophenone (DFAP) have been recorded in the regions 4000–400cm−1 and 3500–50cm−1, respectively. Utilizing the observed FTIR and FT-Raman data, a complete vibrational assignment and analysis of the fundamental modes of the compound were carried out. The optimum molecular geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, were calculated by density functional theory (DFT/B3LYP) method with 6-31+G(d,p) and 6-311++G(d,p) basis sets. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. A detailed interpretation of the infrared and Raman spectra of DFAP is also reported based on total energy distribution (TED). Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The MEP map shows the negative potential sites are on oxygen atom as well as the positive potential sites are around the hydrogen atoms. The UV–Vis spectral analysis of DFAP has also been done which confirms the charge transfer of DFAP. The chemical shifts of H atoms and C atoms were calculated using NMR analysis. Furthermore, the polarizability, the first hyperpolarizability and total dipole moment of the molecule have been calculated.

Synthesis, characterization, thermal behavior, and DFT aspects of some oxovanadium(IV) complexes involving ONO-donor sugar Schiff bases

Seven new Schiff base complexes of oxovanadium(IV), [VO(L)(H2O)], where H2L = H2bmpph-gls, H2bumpph-gls, H2iso-vmpph-gls, H2pmpph-gls, H2iso-bumpph-gls, H2ampph-gls, and H2vmpph-gls, have been synthesized by the reaction of VOSO4·5H2O and the said ligands in aqueous ethanol. The resulting complexes have been characterized on the basis of elemental analysis, vanadium determination, molar conductance, magnetic measurements, thermogravimetric (TG) analysis, infrared, electronic mass, and electron spin resonance studies. The thermal decomposition processes of one representative complex is discussed, and the order of reaction (n) and the activation energies (Ea) have been calculated from TG and differential TG curves. Molecular geometry optimizations, molecular surface electrostatic potentials, vibrational frequency calculations, bond lengths, bond angles and dihedral angles, and natural atomic charges obtained by natural bond orbital and Mulliken population analysis and calculations of molecular energies, highest occupied molecular orbital and lowest unoccupied molecular orbital were performed with the Gaussian 09 software package using density functional theory methods with Becke3–Lee–Yang–Parr (B3LYP) hybrid exchange–correlation functional and the standard 6-311G(+) basis set for (ampph-glsH2) and LANL2DZ basis set for one of its complexes, [VO(ampph-gls)(H2O)]. No imaginary frequency was found in the optimized model compounds, and hence it ensures that the molecule is in the lowest point of the potential energy surface, that is, an energy minimum. Finally calculated results were applied to simulate infrared spectra which show good agreement with observed spectra. Based on experimental and theoretical data, suitable square pyramidal structures have been proposed for these complexes.

Exploring QSARs of some benzenesulfonamides incorporating cyanoacrylamide moieties as a carbonic anhydrase inhibitors (specifically against tumor-associated isoforms IX and XII)

Benzenesulfonamides incorporating cyanoacrylamide moieties with activity against tumour-associated human (h) isoforms hCA IX and XII (which are validated antitumor targets) were investigated for their quantitative structural activity relationships (QSAR). Multiple linear regression analysis was used to develop model relationships between molecular descriptors and inhibition constants (Ki). The molecular geometry optimization were performed on all molecules at DFT-B3LYP/6-311++G(d,p) level. Over 1250 molecular descriptors were calculated using Gaussian 09, Hyperchem and EDRAGON programs. Multiple linear regression equations have been developed and validated using leave-one-out cross-validated technique. The derived QSAR models are found to be statistically significant and show good predictive ability.

Electrostatic Forces: Formulas for the First Derivatives of a Polarizable, Anisotropic Electrostatic Potential Energy Function Based on Machine Learning

Explicit formulas are derived analytically for the first derivatives of a (i) polarizable, (ii) high-rank multipolar electrostatic potential energy function for (iii) flexible molecules. The potential energy function uses a machine learning method called Kriging to predict the local-frame multipole moments of atoms defined via the Quantum Chemical Topology (QCT) approach. These atomic multipole moments then interact via an interaction tensor based on spherical harmonics. Atom-centered local coordinate frames are used, constructed from the internal geometry of the molecular system. The forces involve derivatives of both this geometric dependence and of the trained kriging models. In the near future, these analytical forces will enable molecular dynamics and geometry optimization calculations as part of the QCT force field.

An efficient synthesis of novel l-rhamnose based non-ionic surfactants under controlled microwave irradiation

The scope and limitations of microwave-assisted glycosylation for the preparation of various alkyl l-rhamnoside amphiphiles were investigated. Straightforward coupling of hydrophilic unprotected sugar and hydrophobic high molecular weight alcohols, in the presence of p-toluenesulfonic acid as a promoter, yielded structurally different compounds in very good yields (37–87%). A homologous series including 17 examples of alkyl α-l-rhamnoside amphiphiles varying in chain structure (C4–C20) is reported. The structures of the new derivatives were determined by NMR spectroscopy and quantum chemical calculations. Molecular geometry optimizations of different ring forms (1C4 and 4C1) and anomeric configurations were carried out using DFT calculations. Herein we demonstrate the advantages of microwave irradiation for the preparation of a broad variety of linear and branched-chain alkyl α-l-rhamnosides. The application of this approach to the synthesis of new natural non-ionic surfactants makes this method attractive because of their potential use in biomedical and pharmaceutical chemistry.

Optical Absorption of the Antitrypanocidal Drug Benznidazole inWater

UV-vis optical absorption spectra of the antitrypanocidal drug benznidazole solvated in water were measured for various concentrations. The spectra show a prominent peak around 3.80 eV, while deconvolution of the UV-vis optical absorption spectra revealed six bands centered at 3.60, 3.83, 4.15, 4.99, 5.60, and 5.76 eV. Benznidazole electronic transitions were obtained after density functional theory (DFT) calculations within the polarized continuum (PCM) model for water solvation. Molecular geometry optimizations were carried out, and the measured absorption peaks were related to specific molecular orbital transitions obtained within the time dependent DFT (TD-DFT) with excellent agreement between theory and experiment.

Vibrational spectroscopic study, charge transfer interaction and nonlinear optical properties of l-asparaginium picrate: A density functional theoretical approach

Single crystals of L-asparaginium picrate (LASP) were grown by slow evaporation technique at room temperature and were the subject of an X-ray powder diffraction study to confirm the crystalline nature of the synthesized compound. FT-IR and Raman spectra were recorded and analyzed with the aid of the density functional theory (DFT) calculations in order to make a suitable assignment of the observed bands. The optimum molecular geometry, normal mode wavenumbers, infrared and Raman intensities and the first hyperpolarizability were investigated with the help of B3LYP method using 6-31G(d) basis set. The theoretical FT-IR and Raman spectra of LASP were simulated and compared with the experimental data. A good agreement was shown and a reliable vibrational assignment was made. Natural bond orbital (NBO) analysis was carried out to demonstrate the various inter and intramolecular interactions that are responsible for the stabilization of the title compound leading to high NLO activity. A study on the electronic properties was performed by time-dependent DFT (TD-DFT) approach. The lowering in the HOMO and LUMO energy gap explains the eventual charge transfer interactions that take place within the molecules.

Surface-enhanced Raman scattering and DFT investigation of 1,5-diphenylcarbazide and its metal complexes with Ca(II), Mn(II), Fe(III) and Cu(II)

In recent years, surface-enhanced Raman scattering (SERS) has become an increasingly viable method for the detection of metal ions, evidenced by the existing studies on metal complexes. In this study, 1,5-diphenylcarbazide (DPC) and its Ca(II), Mn(II), Fe(III) and Cu(II) complexes were investigated by FTIR/ATR, FT-Raman and surface-enhanced Raman spectroscopies. The hybrid B3LYP exchange–correlation functional was used for the molecular geometry optimizations, molecular electrostatic potential (MEP) distribution and vibrational frequencies calculations of the DPC molecule and its complexes. Based on experimental and theoretical data, we were able to accurately identify unique and representative features for each DPC–metal complex, features that enable the detection of said metal complexes in millimolar concentrations.

Structure investigation of mesalazine drug using thermal analyses, mass spectrometry, DFT calculations, and NBO analysis

Mesalazine (MZ) drug has been used for several decades as a primary treatment for inflammatory bowel diseases. The drug was investigated using thermal analysis (TA) measurements and electron impact mass spectral fragmentation at 70 and 15 eV of electron energy. The optimum molecular geometry and the total energy of the neutral and the positively charged MZ molecules were calculated by density functional theory method with 6-311++G(d,p) basis sets. Stability of the molecules arising from hyperconjugative interactions, charge delocalization, and the natural atomic charges has been analyzed using natural bond orbital analysis. In electron ionization mass spectrometry, the primary rupture is due to successive loss of H2O (OH from carboxyl and H from phenolic OH of the ring) and CO of the acetyl group. Thermogravimetric results have revealed two stages of mass loss at 75.3 and 25.3 % in ranges 225–350 and 350–650 °C, respectively. The first one may be due to successive losses of different groups or molecules with fast rate of decomposition. A comparison between MS and TA helped in selection the proper pathway representing the fragmentation mechanism of this drug.

The Complexation of the Anticancer Drug ThioTEPA with Methylated DNA Base Guanine: Combined Ab Initio and QTAIM Investigation.

Non-covalent complexes of methylated nitrogenous DNA base guanine (m(9) Gua) with 1 to 6 molecules of anticancer drug ThioTEPA (1,1',1''-phosphorothioyltriaziridine) have been investigated by molecular modeling techniques (molecular docking and DFT geometry optimization), ab initio wavefunction calculations and the quantum theory of atoms in molecules (QTAIM). The accuracy of complex structures predicted by standard molecular docking techniques have been assessed by comparing them with ab initio calculations, and the most important differences have been discussed. Obtained stabilization enthalpies (kcal/mol) for the m(9) Gua⋅⋅⋅(ThioTEPA)n complexes with n=1…6 have been found to be -15.6, -26.5, -38.4, -49.6, -60.5 and -69.3 respectively. The non-covalent interactions revealed by the QTAIM method have been shown to be a dominating factor responsible for the complex stability, with hydrogen bonds of NH⋅⋅⋅N type being the most important interactions in small (n=1 to 4) and CH⋅⋅⋅N bonds - in large (n=5, 6) complexes. The obtained results may help to understand ThioTEPA-DNA interactions and clarify the mechanism of the drug action.

In Silico Design of Monomolecular Drug Carriers for the Tyrosine Kinase Inhibitor Drug Imatinib Based on Calix- and Thiacalix[n]arene Host Molecules: A DFT and Molecular Dynamics Study.

The use of functionalized calix- and thia-calix[n]arenes is proposed as the basis for our in silico design of a suitable drug carrier for the tyrosine kinase inhibitor, Imatinib. Their mutual electronic properties and interaction energies, Eint, were assessed with the use of Density Functional Theory (DFT) methods under the NBODel methodology. Three structural variables for the host molecules were considered: R = {SO3H (1), t-Bu (2), i-Pr (3), COOH (4), (CH2)2OH (5), (CH2)2NH2 (6)}; b = {CH2, S}; n = {5, 6, 8}, and two possible orientations for the insertion of Imatinib within the macrocycle cavity: pyridine moiety pointing inward (N1) and piperazine pointing inward (N2). In total, we explored 72 different assemblies. Initial molecular mechanics geometry optimizations with the UFF potential were undertaken for every host-guest complex, with further optimization at the B97D/6-31G(d,p) level of theory. Using the same optimized structures, Molecular Dynamics (MD) simulations were carried out on all 72 assemblies using the General Amber Force Field and the AMBER 12 MD package. Electronic parameters were fitted using the RESP method, and the complexes were run for 100 ns. Potential of mean force was obtained for the most stable systems using umbrella sampling and the Weighted Histogram Analysis Method. Calix[n]arenes families 1 and 5 (R = SO3H and (CH2)2OH, respectively) with n = 6 constitute the most promising candidates to become drug carriers within our parameter space due to their more negative Eint values and increased flexibility to allow the inclusion of the drug.

Thermodynamic properties of 1-phenylnaphthalene and 2-phenylnaphthalene

Measurements leading to the calculation of thermodynamic properties in the ideal-gas state for 1-phenylnaphthalene (Chemical Abstracts registry number [605-02-7]) and 2-phenylnaphthalene (Chemical Abstracts registry number [612-94-2]) are reported. Experimental methods for 1-phenylnaphthalene were adiabatic heat-capacity calorimetry, differential scanning calorimetry, inclined-piston manometry, comparative ebulliometry, vibrating-tube densitometry, and combustion calorimetry. For 2-phenylnaphthalene, the experimental methods were adiabatic heat-capacity calorimetry, differential scanning calorimetry, and comparative ebulliometry. Critical properties were estimated for both compounds. Molar thermodynamic functions (enthalpies, entropies, and Gibbs free energies) for the condensed and ideal-gas states were derived from the experimental studies at selected temperatures. Statistical calculations were performed based on molecular geometry optimization and vibrational frequencies calculated at the B3LYP/6-31+G(d,p) and B3LYP/cc-pVTZ levels of theory. Ideal-gas entropies derived with two the independent methods are shown to be in good accord for 1-phenylnaphthalene, but significant differences are apparent for 2-phenylnaphthalene. These differences are likely due to a disorder of unknown type in the crystals of 2-phenylnaphthalene at low temperatures, as evidenced by the presence of a glass-like transition in the measured heat capacities for the solid state. All experimental results are compared with property values reported in the literature.