MM2 Force Research Articles

Design of new molecules against cervical cancer using DFT, theoretical spectroscopy, 2D/3D-QSAR, molecular docking, pharmacophore and ADMET investigations

Cervical cancer is a major health problem of women. Hormone therapy, via aromatase inhibition, has been proposed as a promising way of blocking estrogen production as well as treating the progression of estrogen-dependent cancer. To overcome the challenging complexities of costly drug design, in-silico strategy, integrating Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD), was applied to large representative databases of 39 quinazoline and thioquinazolinone compound derivatives. Quantum chemical and physicochemical descriptors have been investigated using density functional theory (DFT) and MM2 force fields, respectively, to develop 2D-QSAR models, while CoMSIA and CoMFA descriptors were used to build 3D-QSAR models. The robustness and predictive power of the reliable models were verified, via several validation methods, leading to the design of 6 new drug-candidates. Afterwards, 2 ligands were carefully selected using virtual screening methods, taking into account the applicability domain, synthetic accessibility, and Lipinski's criteria. Molecular docking and pharmacophore modelling studies were performed to examine potential interactions with aromatase (PDB ID: 3EQM). Finally, the ADMET properties were investigated in order to select potential drug-candidates against cervical cancer for experimental in vitro and in vivo testing.

In vitro α-amylase and α-glucosidase inhibition study of dihydropyrimidinones synthesized via one-pot Biginelli reaction in the presence of a green catalyst

A green catalyst WELPSA-catalyzed three-component condensation (Biginelli) process involving an aldehyde, barbituric/thiobarbituric/1,3-dimethylbarbituric acid, and urea/thiourea/guanidine hydrochloride in a single pot in presence of a green solvent for the production of DHPM have been presented. The catalyst is reusable and this methodology is scalable. By using the in vitro experiments, the antidiabetic potentiality of synthesized compounds that inhibit α-amylase along with α-glucosidase efficiencies was assessed. All the synthesized compounds except for 4a and 4e, showed the most significant inhibition for α-amylase and α-glucosidase activities. Among the synthesized DHPM compounds, 4c and 4b exhibited significant inhibition profiles compared to the standard antidiabetic drug acarbose. Furthermore, synthesized substances' energy-minimized structures, 3D structures, and DFT calculations were performed using Gaussian 09 software, hybrid models, and MM2 force approaches. Strong hydrogen bonds with amino acid residues Arg-672, Arg-600, Trp-613, Asp-404, Asp-282, and Asp-616 indicate that an α-glucosidase-inhibitory peptide may have hypoglycemic efficacy confirmed by the molecular docking study of the synthesized DHPM.

Exploring the impact of electron acceptor tuning in D-π-A′-π-A photosensitizers on the photovoltaic performance of acridine-based DSSCs: A DFT/TDDFT perspective

Nine novel organic molecules with D-π-A′-π-A motifs, designated as (Ac-T-Qs-T-CA) and (Ac-T-Bx-T-CA), were proposed as potential photosensitizers for use in dye-sensitized solar cells (DSSCs). These novel organic photosensitizers are comprised of an acridine electron donor (Ac) and a thiophene π-spacer (T), while the electron acceptor unit (A′) is either a substituted quinoxaline (Qs) or a benzo[2,5]diazole-1-heteroatom (Bx), and the anchoring group (A) is 2-cyanoacrylic acid (CA). The influence of electron acceptor (A′) moieties on the electronic, photophysical, thermodynamic and photovoltaic properties of the photosensitizers was analyzed using DFT and TD-DFT calculations. The MM3 force field and CONFLEX conformational search methods were employed to study all possible structural conformations of the photosensitizers. The goal was to identify the lowest energy conformer and gain a better understanding of how the structure conformation and torsional angles of (Ac-T-Qs-T-CA) and (Ac-T-Bx-T-CA) compared to the reference photosensitizer RK1 affect electron injection ability and overall performance of DSSCs. The thermodynamic analysis revealed that the photosensitizers (Ac-T-Q2,3-diOMe-T-CA) and (Ac-T-BtA-T-CA), which contain a 2,3-dimethoxyquinoxaline (Q2,3-diOMe) and a benzo[d][1,2,3]triazole (BtA) acceptor moieties, respectively, exhibit a noteworthy enhancement in their electron-injection free energy (ΔGinj) and a reduction in their recombination-free energy (ΔGrec) values, leading to an improvement in the overall photovoltaic properties of the solar cell when compared to the other photosensitizers. The photovoltaic characteristics of the photosensitizers showed that the photosensitizer (Ac-T-Q2,3-diOMe-T-CA) demonstrated the highest values of open-circuit photovoltage (Voc = 1.41 eV) and light harvesting efficiency (LHE = 0.80 eV) compared to the other (Ac-T-Qs-T-CA) photosensitizers. Similarly, (Ac-T-BtA-T-CA) photosensitizer demonstrated the highest Voc (1.08 eV) and LHE (0.75 eV) among (Ac-T-Bx-T-CA) photosensitizers. The photovoltaic performance of these new photosensitizers outperformed the reference RK1 photosensitizer, which only achieved a Voc of 1.2 eV and LHE of 0.61 eV. Finally, the electronic structures and optical properties of photosensitizers adsorbed on the TiO2 surface were studied to provide more accurate information about their adsorption on the semiconductor surface.

Quantitative structure activity relationship (QSAR) modeling study of some novel thiazolidine 4-one derivatives as potent anti-tubercular agents

This study aims to develop a QSAR model for Antitubercular activity. The quantitative structure-activity relationship (QSAR) approach predicted the thiazolidine-4-ones derivative’s Antitubercular activity. For the QSAR study, 53 molecules with Antitubercular activity on H37Rv were collected from the literature. Compound structures were drawn by ACD/Labs ChemSketch. The energy minimization of the 2D structure was done using the MM2 force field in Chem3D pro. PaDEL Descriptor software was used to construct the molecular descriptors. QSARINS software was used in this work to develop the 2D QSAR model. A series of thiazolidine 4-one with MIC data were taken from the literature to develop the QSAR model. These compounds were split into a training set (43 compounds) and a test set (10 compounds). The PaDEL software calculated 2300 descriptors for this series of thiazolidine 4-one derivatives. The best predictive Model 4, which has R 2 of 0.9092, R 2adj of 0.8950 and LOF parameter of 0.0289 identify a preferred fit. The QSAR study resulted in a stable, predictive, and robust model representing the original dataset. In the QSAR equation, the molecular descriptor of MLFER_S, GATSe2, Shal, and EstateVSA 6 positively correlated with Antitubercular activity. While the SpMAD_Dzs 6 is negatively correlated with Antitubercular activity. The high polarizability, Electronegativities, Surface area contributions and number of Halogen atoms in the thiazolidine 4-one derivatives will increase the Antitubercular activity.

Interaction of Components of Epoxy Composite Containing Carbon Nanotubes and Graphene Oxide Mixture

Mixtures of carbon nanotubes (CNTs) and graphene oxide (GO) in composite materials often exhibit synergistic effects with respect to mechanical and electrophysical properties. In this paper, the mechanisms of interaction between CNTs, GO and epoxydian resin macromolecules were discussed based on the results of molecular dynamics simulations. Calculations were performed in the MM3 force field at exposure times up to 100 ps. The influence of the CNT’s graphene layers shape and the presence of oxygen-containing functional groups on the self-assembly process during the epoxy composite formation has been demonstrated. It is shown that graphene oxide sheets are arranged around cylindrical nanotubes and envelop them, while when using tapered nanotubes, the formation of alternating layers of CNTs and GO should be expected. The presence of oxygen-containing groups on the surface of cylindrical nanotubes promotes the penetration of epoxydian resin macromolecules into the space between CNTs and GO. The simulation results of the "cylindrical CNTs - GO" and the "conical CNTs - GO" hybrid particles were confirmed by scanning electron microscopy data.

An investigation on the structure and group vibrations of balenine molecule by matrix isolation IR spectroscopy, DFT and MP2 based calculations

Stable conformers of neutral balenine were scanned through molecular dynamics simulations and energy minimizations using Allinger’s MM2 force field. For each of the found minimum-energy conformers, geometry optimization and thermochemistry calculations were performed by using B3LYP, MP2, G3MP2B3 methods, 6-31G(d), 6–311++G(d,p) and aug-cc-pvTZ basis sets. The calculation results have indicated that balenine has about twenty stable conformers whose relative energies are in the range of 0–9.5 kcal/mol. Three of these are thought to provide the major contribution to matrix isolation IR spectra of the molecule. Our solvent calculations using the polarized continuum model revealed the stable zwitterion structures which are predicted to dominate IR spectra of balenine in water and heavy water (D2O) solvents. Pulay’s SQM-FF method was used in scaling of the harmonic force constants and vibrational spectral data calculated for the neutral and zwitterion structures. These refined calculation data together with those obtained from anharmonic frequency calculations enabled us to correctly interpret the matrix isolation IR spectrum of balenine and the tautomerism-based changes observed in its KBr IR and solution (D2O) IR spectra. The results revealed the crucial role of conformation and zwitterionic tautomerism on the structure and vibrational spectral data of the molecule.

In silico analysis of ciprofloxacin analogs as inhibitors of DNA gyrase of Staphylococcusaureus

In this in silico study, thirty-five ciprofloxacin analogs were docked to the active site of DNA gyrase, the prime target of ciprofloxacin type antibiotics. Prior to docking all the structures were optimized using MM2 force field parameters. The study revealed that five candidates, namely 6MePQ_3, 6MePQ_11, A6MePQ_3, HPQ_11, and PQ_7, exhibited promising binding to DNA gyrase. Upon analysis of the ligand-receptor complex, it is also divulged that this binding has been stabilized by the interaction between different neutral, nonpolar, aromatic amino-acid residues of DNA gyrase and the ciprofloxacin analogs. Moreover, the interaction between ciprofloxacin analogs and DNA gyrase was mainly governed by hydrophobic interactions and, to a lesser extent, hydrogen bonds. Halogen bonds, electrostatic interactions, and other types of interactions were almost absent in all cases. Molecular dynamic simulation was performed to recognize the structural variations and the complexes' stability of suggested ligands. This study indicates that 6MePQ_3 forms a stable drug-protein complex. On the other site, Pharmacokinetic filtering done using SwissADME server, reveals that 6MePQ_3 is well absorbed from the GI tract, does not cross BBB and is not a P-gp substrate. But it is possible to check and confirm its all “in silico” pharmacodynamics and pharmacokinetics characteristics in real life by synthesis and subsequent analysis of this ligand.

Synthesis, Spectroscopic, Molecular Modeling and Anti-Fungal Studies of Some Divalent Metal Complexes of 4-Hydroxyacetophenone Isonicotinoyl Hydrazone

A novel ligand N-4-hydroxyacetophenone isonicotinoyl hydrazone and its manganese(II) and nickel(II) metal complexes have been synthesized. The synthesized Schiff base and its metal complexes have been characterized by physical state determination, melting point and solubility measurements in different solvents, infrared, proton nuclear magnetic resonance, mass spectrometric and powder X-ray spectroscopic techniques. The thermal properties of the prepared compounds were obtained from TG/DTG measurements. On the basis of the analytical techniques, the ligand was found to be bidentate in nature coordinating to the metal ions through the azomethine nitrogen and carbonyl oxygen atoms leading to distorted octahedral geometries of the metal complexes which were modeled using MM2 force field. The ligand and its metal(II) complexes were evaluated for antifungal activity against Aspergillus fumigatus, Aspergillus niger, Candida albicans and Rhizopus stolonifera. The antifungal evaluation results revealed an enhanced activity upon coordination of the ligand with the metal(II) ions. The activity of the metal complex to the tested fungal strains was in the order Ni(II) > Mn(II).

Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19).

COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many people have been contaminated by environmental contamination and transmission from one human to another until now. The objective of the present work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein), using molecular docking approach. The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore, and H Bond score of nicotiflorin and standard inhibitor X77 were observed as -173.058, -127.302, -21.9398 and -156.913,-121.296,-5.7369, respectively. Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.

Topological Analysis of Electron Density in Large Biomolecular Systems.

A great step toward describing the structure of the molecular electron was made in the era of quantum chemical methods. Methods play a very important role in the prediction of molecular properties and in the description of the reactivity of compounds, which cannot be overestimated. There are many works, books, and articles on quantum methods, their applications, and comparisons. At the same time, quantum methods of a high level of theory, which give the most accurate results, are time-consuming, which makes them almost impossible to describe large complex molecular systems, such as macromolecules, enzymes, supramolecular compounds, crystal fragments, and so on. To propose an approach that allows real-time estimation of electron density in large systems, such as macromolecules, nanosystems, proteins. AlteQ approach was applied to the tolopogical analysis of electron density for "substrate - cytochrome" complexes. The approach is based on the use of Slater's type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of "CYP3A4 - substrate" complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular "CYP3A4 - substrate" space was performed. Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. Relationship of pKM (KM is Michaelis constant) with the maximal value of the second Laplacian eigen value of electron density at the critical points and energy of complex formation computed using MM3 force field was determined. It was shown that significant number of (3,-1) bond critical points are located in the intermolecular space between the enzyme site and groups of substrate atoms eliminating during metabolism processes.

Correlation between single crystal data and molecular mechanics calculation of 3-(2-hydroxy-phenylimino)-1,3-diphenyl-propan-1-one

The Schiff base 3-(2-hydroxy-phenylimino)-1,3-diphenyl-propan-1-one (L), was prepared and characterized by elemental analysis, IR, 1H NMR and mass spectral techniques. The crystal and molecular structures were determined by using the single crystal X-ray diffraction data. The crystal was triclinic with unit-cell dimensions: a = 9.051(3) Å, b = 10.245(3) Å, c = 11.016(3) Å, α = 69.28(2)°, β = 81.66(2)°, γ = 64.25(2)°, space group is Pī and Z = 2. The structure was refined by least squares method. The single crystal was prepared by supersaturating method using tetramethoxysilane as gelling agent. Energy minimization for locating stable conformations and single point energy calculations for comparing the obtained and calculated conformations of the same molecule were carried out using molecular mechanics method (MM2 force field). The bond lengths and the bond angles were calculated and compared with the values obtained from the single crystal analysis. The obtained results were discussed and evaluated. Generally, the calculated parameters are in good agreement with the corresponding X-ray diffraction values. The obtained results reveal that, the amine-imine tautomerism is more preferable than keto-enol form and the intra-hydrogen bond stabilize the amine-imine tautomerism.

Anharmonic Molecular Mechanics: Ab Initio Based Morse Parametrizations for the Popular MM3 Force Field

Methodologies for creating reactive potential energy surfaces from molecular mechanics force-fields are becoming increasingly popular. To date, molecular mechanics force-fields in biochemistry and small molecule organic chemistry tend to use harmonic expressions to treat bonding stretches, which is a poor approximation in reactive and nonequilibirum molecular dynamics simulations since bonds are often displaced significantly from their equilibrium positions. For such applications there is need for a better treatment of anharmonicity. In this contribution, Morse bonding potentials have been extensively parametrized for the atom types in the MM3 force field of Allinger and co-workers using high level CCSD(T)(F12*) energies. To our knowledge this is among the first instances of a comprehensive parametrization of Morse potentials in a popular organic chemistry force field. In the context of molecular dynamics simulations, these data will: (1) facilitate the fitting of reactive potential energy surfaces using empirical valence bond approaches and (2) enable more accurate treatments of energy transfer.

Electron momentum spectroscopy of cyclopentane: A molecular dynamical investigation

The experimental results of electron momentum spectroscopy studies on the valence orbitals of cyclopentane have been reinterpreted on the basis of Molecular Dynamical simulations employing the classical MM3 force field. Analysis using the produced molecular structures demonstrates that the pseudorotation and the variations of the ring puckering amplitude due to thermally induced vibrational effects have significant influence on the electron momentum distributions for the six highest-energy orbitals 1e2″, 3e1′ and 3e2′. The conformational average of the structures of C2 symmetry and the structures of Cs symmetry is also an equitable model to interpret the valence electron momentum distributions.

Conformational space of 4,4′-methoxypropylstilbene molecule

Quantum-chemical simulation of the ground state [the density function B3LYP/6-31G, B3LYP/6-31G(d), and B3LYP/6-31+G(d,p) and the perturbation theory MP2/6-31G(d) methods] and the transition states [the B3LYP/6-31G(d) method] of 4,4′-methoxypropylstilbene molecule has been performed. Using the Ellinger MM2 force field method, the potentials of internal rotation have been obtained for each rotational degree of freedom of the molecule. The B3LYP simulation has revealed the planarity of the conjugated system and the orthogonal position of the alkyl substituent, whereas the benzene rings have deviated by about 20° with respect to the double bond plane according to the MP2 data. Three transition states of the molecule corresponding to the saddle points of the first and the second orders have been revealed. The stationary points have been identified by means of vibrational analysis.

Hydrogen Bonding in Tight Environments: Simulated Force Spectroscopy of Nanoconfined Hydrogen-Bonded Complexes

The single-molecule force spectroscopy of a prototypical class of hydrogen-bonded complexes is computationally investigated. The complexes consist of derivatives of a barbituric acid and a Hamilton receptor that can form up to six simultaneous hydrogen bonds. The force–extension (F–L) isotherms of the host–guest complexes are simulated using classical molecular dynamics and the MM3 force field, for which a refined set of hydrogen bond parameters was developed from MP2 ab initio computations. The F–L curves exhibit peaks that signal conformational changes during elongation, the most prominent of which is in the 60–180 pN range and corresponds to the force required to break the hydrogen bonds. These peaks in the F–L curves are shown to be sensitive to relatively small changes in the chemical structure of the host molecule. Thermodynamic insights into the supramolecular assembly were obtained by reconstructing, from the force measurements, the Helmholtz free energy profile along the extension coordinate and ...

The effects of conformation and zwitterionic tautomerism on the structural and vibrational spectral data of anserine

In this study, the stable conformers of neutral anserine were searched by molecular dynamics simulations and energy minimization calculations using the MM2 force field. Thermochemical calculations at B3LYP/6-31G(d) level of theory followed these preliminary calculations. The results confirmed that neutral anserine has quite a flexible structure and many stable gauche and trans conformers at room temperature. Nevertheless, two are considerably more favourable in energy than the others and expected to dominate the gas-phase and matrix IR spectra of the molecule. The corresponding structural and vibrational spectral data for these two conformers of neutral anserine, whose relative stabilities were also examined by high-accuracy energy calculations carried out using G3MP2B3 method, and for the most stable conformer of anserine in zwitterion form were calculated at B3LYP/6-311++G(d,p) level of theory. The calculated harmonic force constants were refined using the Scaled Quantum Mechanical Force Field (SQM-FF) method and then used to produce the refined wavenumbers, potential energy distributions (PEDs) and IR and Raman intensities. These refined data together with the scaled harmonic wavenumbers obtained using another method, Dual Scale factors (DS), enabled us to correctly analyse the observed IR and Raman spectra of anserine and revealed the effects of conformation and zwitterionic tautomerism on its structural and vibrational spectral data.

Conformations of Organophosphine Oxides.

The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P-C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes-an essential part of understanding the chemistry of these compounds. The predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

Application of the molecular mechanics method to simulation of buckling of single-walled carbon nanotubes

The molecular mechanics (MM) method based on the Modified Morse force field is used to determine the critical buckling parameters and post-critical deformation modes of single-walled carbon nanotubes (SWCNTs) twisted at the edges. Computer simulation of the buckling and post-critical deformation of nanotubes is performed using two versions of the MM method: the standard MM method and a mixed method combining the molecular mechanics and molecular structural mechanics approaches (MM/MSM method). Computer simulation shows that the MM/MSM method gives acceptable critical twisting angles, buckling modes, and post-critical deformed configurations of nanotubes, comparable to the critical twisting angles, modes, and configurations obtained using the standard MM method. More precisely, for the (10,10) armchair SCWNT 12.2919nm long, the solutions obtained by both methods are similar up to the beginning of fracture of the SCWNT (at a twisting angle up to 240° for each edge), and for the (10,0) zigzag SCWNT 16.8980nm long, the solutions obtained by both methods are similar up to the final twisting angle of 360° for each edge. The critical linear twisting angle for the (10,10) armchair SWCNT obtained in the present study is compared with the critical linear twisting angles obtained by other authors using the REBO, DREIDING, and MM3 force fields. It is concluded that the critical linear twisting angle obtained in the present study using the Modified Morse force field is unrealistically underestimated compared to the critical linear twisting angles obtained by other authors using the REBO, DREIDING, and MM3 force fields.

The effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data of naproxen molecule

The structural and vibrational properties of naproxen, an inhibitor of cyclooxygenase (COX) enzyme, were investigated by molecular modeling and experimental IR and Raman spectroscopic techniques. Possible conformers of the molecule were searched via a molecular dynamics simulation carried out with MM2 force field. The total energies, equilibrium geometries, force fields, IR and Raman spectral data of the found stable conformers were determined by means of geometry optimization and harmonic frequency calculations carried out using the B3LYP method and Pople-style basis sets of different size. The stability order obtained for the lowest-energy conformers was confirmed by high-accuracy thermochemistry calculations performed with G3MP2B3 composite method. Some electronic structure parameters of naproxen and the anharmonicity characters of its vibrational modes were determined by means of natural population analysis (NPA) and anharmonic frequency calculations at B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels of theory. A part of these calculations carried out for free naproxen molecule were repeated also for its energetically most favored dimer forms. Two different scaling procedures ((1) “SQM-FF methodology” and (2) “Dual scale factors”) were independently applied to the obtained harmonic vibrational spectral data to fit them to the corresponding experimental data. In the light of the obtained calculation results, which confirm the remarkable effects of conformation and intermolecular hydrogen bonding on the structural and vibrational spectral data, in particular, on those associated with the functional groups in the propanoic acid chain, a reliable assignment of the fundamental bands observed in the experimental IR and Raman spectra of the molecule was achieved.

Electron Momentum Spectroscopy of 1-Butene: A Theoretical Analysis Using Molecular Dynamics and Molecular Quantum Similarity

The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules.