Hydrogen-bonding effects,electrostatic potential,and the antitumor activity of flavone acetic acid and related compounds. I. Ab initio studies on the first stable conformations

Ab initio investigations have been carried out to account for the antitumor activity of flavone acetic acid (FAA) and related compounds. The hydrogen-bonding conformation was chosen for all the compounds and obtained through a restricted geometry optimization with the 3-21G basis set. Three key regions in the molecular electrostatic potential isosurfaces [V( r ) ～ ?0.015 au] are found to be involved in the activity. Region 1 is the most important. Its existence implies the activity and its size determines the strength of the activity. Region 2 is another factor which can change the strength of the activity. Region 3 corresponds to the hydrogen-bonding effects which have been analyzed in detail, but its role is still not clear. Finally, basis-set effects on the molecular electrostatic potential have been briefly discussed. © 1995 John Wiley & Sons, Inc.     

Hydrogen-bonding effects,electrostatic potential,and the antitumor activity of flavone acetic acid and related compounds. III. Ab initio studies on the conformation space

Restricted geometry optimizations at the ab initio SCF level with the 3-21G basis set were employed to investigate the conformation space of flavone acetic acid (FAA) and its related compounds. All the conformations are produced from a conformation which is, according to our previous work, probably the active conformation in terms of antitumor activity shown by these compounds. Detailed studies on FAA were carried out while only brief discussions are made on the analogs. The main results obtained are that (1) FAA is a very flexible molecule, e.g., with the energy barrier up to about 3 kcal mol⁻¹ from the reference conformation, the important torsional angle τ₁ can change from 27.0° to 117.0°, τ₂ from −168.0° to 2.0°, and τ₃ from −50.0° to 30.0°; (2) the hydrogen-bonding effect plays an important role in determining lower-energy conformations; (3) among all the FAA conformations considered, some are active and some are inactive; (4) it seems that the analogs will have similar behavior to FAA when the torsional angle τ₃ is restricted to the values which are around the equilibrium values; and (5) the hypothesis put forward previously has been further developed in this work. Now, we postulate that efficient charge transfers will lower the energy and that proper charge transfers will activate the molecule. There are mainly two different types of charge transfer corresponding to two different types of conformation, which are specified in this article. © 1997 John Wiley & Sons, Inc.     

A study of hydration effects on the conformational aspects of gaba mediators

The conformation of numerous chemical compounds is strongly influenced by solvents. Knowledge of their structure in solution is necessary, especially for a discussion of the biological and pharmacological activity of the molecules. The neurotransmitters and their agonists and antagonists are known to be flexible molecules that interact with quite distinct receptors. The conformational properties of several GABA (γ-aminobutyric acid) mediators have been studied by the MNDO technique. The optimized geometries of the molecules have been used to study the solvent effects on their conformational properties considering the supermolecule approach for their first hydration shell. A conjectural pharmacophoric pattern for several GABA inhibitors has already been suggested from the molecular electrostatic potentials (MEP ) of several molecules using a localized bond orbital technique. In the present work, MEP calculations have been carried out considering a solvent effect on the MNDO optimized geometries to investigate any deviation from the earlier results.     

Theoretical studies of the mechanism of the action of the neurohypophyseal hormones. I. Molecular electrostatic potential (MEP) and molecular electrostatic field (MEF) maps of some vasopressin analogues

Summary Continuing our theoretical studies of the oxytocin and vasopressin analogues, we have analysed the molecular electrostatic potential (MEP) and the norm of the molecular electrostatic field (MEF) of [1--mercaptopropionic acid]-arginine-vasopressin ([Mpa¹]-AVP), [1-(-mercapto-,-cyclopentamethylene)propionic acid]-arginine-vasopressin ([Cpp]-AVP), and [1-thiosalicylic acid]-arginine-vasopressin ([Ths]-AVP) whose low-energy conformations were calculated in our previous work. These compounds are known from experiment to exhibit different biological activity. The scalar fields mentioned determine the energy of interaction with either charged (MEP) or polar (MEF) species, the energy being in the second case either optimal or Boltzmann-averaged over all the possible orientations of the dipole moment versus the electrostatic field. The electrostatic interactions slowly vanish with distance and can therefore be considered to be the factor determining the molecular shape at greater distances, which can help in both predicting the interactions with the receptor at the stage of remote recognition and in finding the preferred directions of solvation by a polar solvent. In the analysis of the fields three techniques have been used: (i) the construction of maps in certain planes; (ii) the construction of maps on spheres centered in the charge center of the molecule under study and of poles chosen according to the main axes of the quadrupole moment; and (iii) the construction of surfaces corresponding to a given value of potential. The results obtained show that the shapes of both MEP and MEF are similar in the case of [Mpa¹]-AVP and [Cpp¹-AVP (biologically active), while some differences emerge when comparing these compounds with [Ths¹]-AVP (inactive). It has also been found that both MEP and MEF depend even more strongly on conformation.     

Ab initio SCF and MRD CI studies of the FHCl− ion

The equilibrium geometry and hydrogen-bonding energy of the heterobihalide ion FHCl^? have been calculated by ab initio SCF and MRD CI methods using an AO basis set of near Hartree-Fock quality. In the most stable (linear) conformation of this ion, the equilibrium F Cl/FH distances are predicted to be 5.657/1.754, 5.453/L800 and 5.437/1.801 bohr by SCF, MRD CI and full CI (estimated) calculations respectively. A second minimum, which is of extremely small depth and corresponds to the hydrogen atom near the chlorine atom, begins to appear in the potential surface at an FCl distance of about 6.0 bohr. The hydrogen-bonding energy of FHCl^? lies in the range 18–22 kcal/mol.     

Alcohols,ethers, carbohydrates,and related compounds. III. The 1,2-dimethoxyethane system

Ethylene glycol, its dimethyl ether, and some related compounds have been studied using the MM4 molecular mechanics force field. The MM4 calculated structural and energetic results have been brought into satisfactory agreement with a considerable number of experimental data and MP2/6-311++G(2d,2p) ab initio calculations. The heats of formation of these compounds are also well calculated. The MM4 ethylene glycol conformations in particular are in good agreement, both geometrically and in terms of energy, with those from the ab initio calculations. The corresponding dimethyl ether is of special interest, because it has been suggested that the trans-gauche conformation is unusually stable due to the hydrogen bonding of a hydrogen on a methyl group with the more distant oxygen. It is shown in the present work that while this conformation is more stable than might have been expected, the energy is adequately calculated by MM4 without using any hydrogen bonding between the Cbond;H bond and the oxygen. If such hydrogen bonding occurs, it amounts to no more than about 0.5 kcal/mol in energy, and is too small to detect with certainty. Additionally, energetic relationships in trans-1,2-dimethoxycyclohexane, 1,3,5,7-tetraoxadecalin, and 3-methoxytetrahydropyran have been studied, and the calculated results are compared with experimental information, which is adequately reproduced.     

Investigation of binding features: Effects on the interaction between CYP2A6 and inhibitors

A computational investigation has been carried out on CYP2A6 and its naphthalene inhibitors to explore the crucial molecular features contributing to binding specificity. The molecular bioactive orientations were obtained by docking (FlexX) these compounds into the active site of the enzyme. And the density functional theory method was further used to optimize the molecular structures with the subsequent analysis of molecular lipophilic potential (MLP) and molecular electrostatic potential (MEP). The minimal MLPs, minimal MEPs, and the band gap energies (the energy difference between the highest occupied molecular orbital and lowest unoccupied molecular orbital) showed high correlations with the inhibition activities (pIC₅₀s), illustrating their significant roles in driving the inhibitor to adopt an appropriate bioactive conformation oriented in the active site of CYP2A6 enzyme. The differences in MLPs, MEPs, and the orbital energies have been identified as key features in determining the binding specificity of this series of compounds to CYP2A6 and the consequent inhibitory effects. In addition, the combinational use of the docking, MLP and MEP analysis is also demonstrated as a good attempt to gain an insight into the interaction between CYP2A6 and its inhibitors. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

One-pot synthesis,X-ray crystal structure,and identification of potential molecules against COVID-19 main protease through structure-guided modeling and simulation approach

Although antimicrobial resistance before the Covid-19 pandemic is a top priority for global public health, research is already ongoing on novel organic compounds with antimicrobial and antiviral properties in changing medical environments in connection with Covid 19. Thanks to the Biginelli reaction, which allows the synthesis of pyrimidine compounds, blockers of calcium channels, antibodies, antiviral, antimicrobial, anti-inflammatory, or antioxidant therapeutic compounds were investigated. In this paper, we aim to present Biginelli's synthesis, its therapeutic properties, and the structural–functional relationship in the test compounds that allows the synthesis of antimicrobial compounds. Both the DFT and TD-DFT computations of spectral data, molecular orbitals (HOMO, LUMO) analysis, and electrostatic potential (MEP) surfaces are carried out as an add-on to synthetic research. Hirshfeld surface analysis was also used to segregate the different intermolecular hydrogen bonds involved in the molecular packing strength. Natural Bond Orbital (NBO) investigation endorses the existence of intermolecular interactions mediated by lone pair, bonding, and anti-bonding orbitals. The dipole moment, linear polarizability, and first hyperpolarizabilities have been explored as molecular parameters. All findings based on DFT exhibit the best consistency with experimental findings, implying that synthesized molecules are highly stable. To better understand the binding mechanism of the SARS-CoV-2 M^pro, we performed molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations.     

Unsaturated didehydrodeoxycytidine drugs. 1. Impact of C=C positions in the sugar ring

The chemical names of a pair of recently synthesized antitumor drugs are given in the present study as 1',2'-didehydro-3',4'-deoxycytidine and 3',4'-didehydro-2',4'-deoxycytidine. The order of stabilities, geometries, and ionization potentials of the unsaturated sugar-modified cytidine derivatives is investigated quantum mechanically. Our density functional theory calculations based on the B3LYP/6-311++G** model reveal that 3',4'-didehydro-2',4'-deoxycytidine (SD-C2) is slightly more stable than its isomer, 1',2'-didehydro-3',4'-deoxycytidine, by an energy of 5.28 kJ x mol(-1) in isolation. The isomers structurally differ by only the C=C location in the sugar ring. However, the compounds exhibit an unusual orientation with a less puckered sugar ring; that is, 3',4'-didehydro-2',4'-deoxycytidine is determined to be a beta-nucleoside, which is a C1'-endo, north conformer with an anticlinal sugar ring, whereas 1',2'-didehydro-3',4'-deoxycytidine is neither an alpha-nucleoside nor a beta-nucleoside but is a C4'-endo, south conformer with an antiperiplanar sugar ring. The present study further indicates that the C=C double bond location imposes significant effects on their ionization potentials (IPs) and other important molecular properties such as molecular electrostatic potential (MEP). In addition, inner shell binding energy spectral variations with respect to the C=C bond exhibit more site dependence. The valence shell binding energy spectral changes are, on the other hand, significant and delocalized. The latter indicates that such changes in valence space are not isolated effects but are within the entire nucleoside. Finally, the present study suggests that the nearly 0.6 eV difference in the first ionization potentials (highest occupied molecular orbital) of the isomers is sufficiently large to identify them by further spectroscopic measures.     

Study of Radical Polymerization of Arylacetylenes. Composition,Structure, and Some Properties of the Generated Products

Radical polymerization of 2-methyl-5-ethynylpyridine (MEP) and the structure and some properties of phenylacetylene and pentafluorophenylacetylene polymers were investigated. As the first step in polymerization of MEP in the presence of azo-1-cyclohexylcarboxylic acid dinitrile at 94-115°C the monomer conversion is proportional to the quantity of decomposed initiator: 1 mole of initiator causes transformation of 5-7 mole of monomer. At a high degree of polymerization the yield of polymer is not proportional to the initial initiator concentration. The products generated in MEP polymerization initiated thermally or by azo compounds were investigated by means of gel-permeation chromatography, ozonation, ¹H-NMR, IR, and UV spectroscopy. Initiation with azo compounds afforded cyclic trimer (tripicolylbenzene) and a fraction with a number average molecular weight M_n of 1550. Thermal polymerization yielded the dimer (picolyl-substituted quinoline or isoquinoline), tripicolylbenzene, hexaraer, and fractions with M_n = 1500 and 1800. Composition and properties of the polymerization products enable one to assume the presence of poly-MEP hexadiene rings in the main chain. Formation of cyclodiene structures by facile aromatization in the course of arylacetylenes polymerization was confirmed by investigations of the structure and some properties of polyphenylacetylenes and polypentafluoro-phenylacetylenes. A mechanism of radical polymerization of arylacetylenes is proposed.     

Does the proton-transfer reaction take place in the ground state of phenol?(H2O)4 clusters?

In recent experimental studies of infrared (IR) spectra of hydrated phenol clusters, the Mikami and Ebata group at Tohoku University attributed apparently two very different spectra to PhOH(H₂O)₄. The first spectrum has a wide transparent region between 3500 and 3700 cm^-1, which they named a window region. The second spectrum has several absorption bands in this window region. Our previous study revealed that the first spectrum was assigned to the isomers which have a single-ring structure of a hydrogen-bonding network of OH's of phenol and waters. The experimentalists suggested that the second spectrum might be identified to a proton-transferred phenol(SINGLEBOND)water cluster. In the present article, the geometrical structures of proton-transferred hydrated phenol clusters were determined with the ab initio molecular orbital method and their IR spectra were calculated. The proton-transferred phenol(SINGLEBOND)water cluster is at a stable local minimum, but the energy is much higher than that of the most stable nontransferred cluster. The calculated IR spectrum has a still wider window region and is far different from the experimental spectrum of the second type. © 1996 John Wiley & Sons, Inc.     

Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil

Ab initio SCF calculations with the STO -3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.     

The conformation of levopimaric acid investigated by high-level ab initio MO calculations. Possibility of the CH/π hydrogen bond

Ab initio MO calculations were carried out, at the MP2/6-311G(d,p) level of approximation, to investigate the conformation of levopimaric acid. It has been found that the folded conformation is more stable than the extended conformation. The result is consistent with the documented experimental data. The reason for the relative stability of the folded conformation has been sought in the context of the CH/π hydrogen bond. Short non-bond distances have been disclosed between CHs in the 10β angular methyl group and sp² carbons of the conjugated diene ring in the more stable folded conformers of model compounds. We suggest that the folded conformation of levopimaric acid is a consequence of an attractive molecular force, the CH/π hydrogen bond.     

Application of DNMR,group theory and molecular mechanics in the elucidation of the inversion process in the flexible molecule perhydrotetra-azapyrene

The inversion process in cis-10b,10c-perhydro-1H,6H-3a,5a,8a,10a-tetraazapyrene (1) has been investigated by ¹H and ¹³C NMR. The free energy of activation is found to be 14.95 ± 0.2 kcal mole^?1 at 45°. Application of group theoretical techniques led to a graph representing the essential symmetry properties of the potential energy surface for conformational change. The energies of intermediates on this graph were then estimated using molecular mechanics calculations. This combined approach suggests that the total inversion proceeds via a conformation of C_2v symmetry with two non-chair piperazine rings, calculated to be 6.8 kcal mole^?1 less stable than the ground state conformation (C₂ symmetry).     

Laurefurenynes A-F, new Cyclic Ether Acetogenins from a Marine Red Alga, Laurencia sp.

We report here on the discovery and structure determination of three new diastereomeric pairs of cyclic ether acetogenins, laurefurenynes A-F, isolated from the aqueous extract of the alga Laurencia sp. collected in the Philippines. Extensive use was made of NMR spectroscopic data and high resolution MS to determine the structures of the pure compounds. The most stable and the lowest energy conformation was determined using molecular modelling, and their cytotoxic activity was tested against different tumour cells, a significant indication that laurefurenyne C and F are moderately cytotoxic, but non-selective whilst the others are inactive.     

Comparative study of the molecular electrostatic potential obtained from different wavefunctions. Reliability of the semiempirical MNDO wavefunction

A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.     

Retention vs van der walls volume,pi-energy and hydrogen-bonding energy effects and enthalpy in liquid chromatography

Summary The logarithm of capacity ratios (logk’) of alkanes, alkyl alcohols, alkylbenzenes, halogenated benzenes and polyaromatic hydrocarbons are measured in reversedphase liquid chromatography at several temperatures using an octadecyl-bonded silica gel as the packing and acetonitrile/water mixtures as the eluent. The Δ (logk’) values are related to their van der Waals volumes, pi-energy and hydrogen-bonding energy effects and their enthalpies. The difference between the observed capacity ratios and the capacity ratios predicted from van der Waals volumes, pi-energy and hydrogen-bonding energy effects can be explained due to enthalpy effect of larger molecular size compounds. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Quantum-mechanical and molecular mechanics conformational analysis of 1,5-cyclooctadiene

The 1,5-cyclooctadiene (COD) molecule can easily form complexes with transition metals with the molecular structure of various of these complexes being proposed with the aid of X-ray diffraction methods. The fact that the complexes exhibit weak metal-COD bonds makes it very important in inorganic synthesis and catalysis. In this work the potential energy surface (PES) for the COD molecule was comprehensively investigated: first with molecular mechanics (using the MM3 force field); and, in a second stage, at the ab initio Hartree-Fock level of theory employing the 3-21G^*, 6-31G, and 6-31G^* basis sets and also including electron correlation effects at the Moller-Plesset second-order perturbation theory level. This work revealed that there are three distinct conformers of the COD molecule with the predicted lowest energy conformation being in agreement with the proposed structure based on experimental electron diffraction data. © 1997 by John Wiley & Sons, Inc.     

Acridine derivatives. IV. Synthesis,molecular structure,and antitumor activity of the novel 9-anilino-2,3-methylenedioxyacridines

In the biological and physical investigation of a new class of deoxyribonucleic acid (DNA)-intercalating antitumor agents, novel 9-anilino-2,3-methylenedioxyacridines (twelve compounds) have been synthesized and evaluated for the activity against L1210 leukemia in vivo. A few of them possessed the same potency of the antitumor activity as 4′-(9-acridinylamino)methanesulfonyl-m-anisidine (amsacrine, m-AMSA), which is an important antitumor agent in clinical use. The molecular structure of a typical one, 9a in this series have been determined by the X-ray diffraction method using a single crystal. The results of this X-ray investigation have shown that the new class of acridine derivatives have the methylenedioxy group fused at the 2- and 3-positions of the acridine ring.     

Molecular orbital theory of the hydrogen bond. XXX. Water-cytosine complexes

Ab initio SCF and SCF -CI calculations with the STO -3G basis set have been performed to investigate the structures and energies of water–cytosine complexes and the intermolecular water–cytosine surface in the cytosine molecular plane. Although there are six nominal hydrogen-bonding sites in this plane, only three dimers are distinguishable in the ground state. The most stable has an energy of ?10.7 kcal/mol, and is found in the N₁? H and O₂ region. An asymmetric cyclic structure in which the water molecule bridges adjacent N₁? H and O₂ sites is the preferred form of this dimer. The dimer in the region between O₂ and N₄? H′ of the amino group is slightly less stable at ?10.4 kcal/mol, and also has an asymmetric cyclic structure as the preferred structure, with the water molecule bridging amino N₄? H′ and N₃ hydrogen-bonding sites. The third dimer has the amino group as the proton donor to water through the hydrogen cis to C₅, and a stabilization energy of ?7.0 kcal/mol. The water-cytosine surface is characterized by deeper minima and higher barriers than the water-thymine surface and by a decreased mobility of the water molecule between adjacent hydrogen-bonding sites. Absorption of energy by the C₂?O group leads to the first n → π* excited state in which interactions of water with O₂ are broken. The water-cytosine dimers remain bound in this state, but may change structurally. In the second n → π* state interactions between water and N₃ are no longer stabilizing. As a result, the dimer in the O₂ and N₄? H′ region collapses to either a dimer with water the proton donor to O₂, or one with N₄? H′ the proton donor to water. The other two dimers remain bound. All excited dimers are destabilized on vertical excitation relative to the ground state.