Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.     

Investigate oxoazolidine-2,4-dione based eutectic mixture via DFT calculations and SAR

In this work, DFT calculations for the designed eutectic mixtures (EMs) using oxoazolidine 2,4-dione (OZD) and zinc chloride (ZnCl2) are done. The interaction between the hydrogen bond donor and hydrogen bond acceptor at atomic level to get EMs are studied using DFT calculations. At room temperature, the stability of these various systems have been investigated using thermodynamic values or parameters such as enthalpy, free energy and others. DFT calculations is used to investigate the possibility of forming the systems (EMs). Further, the impact of varying the temperature on each system was also investigated (323K, 348K). Various other thermodynamic parameters are studied like dipole moment, hardness, chemical potential of the systems (individual molecules and EMs) at different temperatures. The results of the calculations showed that O1Z4 and O4Z1 have maximum dipole moment having values 8.1291, 9.8801 respectively, indicating maximum polarizability. Change in free energy for O1Z4 is least and was found to be ?37.2496 kcal/ mol. Further on changing the temperature, the parameters do not show much variation. Additionally, we have analyzed structure activity relationship (SAR) method to understand the physico-chemical properties of designed EMs and predict their regression and correlation to optimized energy. From the calculated values of pOE model, the value of r² is 0.9995 confirms the validity of the equation obtained. The results of this study suggest a link between the structures that have been utilized to describe the intermolecular interaction between the hydrogen bond donor and acceptor, as well as the stability of the EMs.     

Ab initio calculation of the interaction energy in the P2 binding pocket of HIV‐1 protease

Interactions at the P2 binding pocket of human immunodeficiency virus type 1 (HIV‐1) protease have been studied using calculated interaction energies for model systems that mimic this binding pocket. Models were built for the P2 pocket of HIV‐1 protease in complex with TMC114, nelfinavir, and amprenavir. A two‐step procedure was applied. In the first step, the size of the model system was confined to ～40 atoms, and the interaction energy was calculated at different computational levels. In the second step, the size of the system was increased to 138 atoms, and the calculations were only performed at the HF/6‐31G** level. The interaction energy of the HIV‐1 protease/TMC114 complex was found to be more favorable than the interaction energies of the other complexes because of the additional hydrogen bond interaction this inhibitor is able to make with the HIV‐1 protease backbone. The results of the calculations are supported by stockholder charges and electrostatic potential maps. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

The role of macrocyclic ligands in the peroxo/superoxo nature of Ni–O2 biomimetic complexes

The impact of the macrocyclic ligand on the electronic structure of two LNi? O₂ biomimetic adducts, [Ni(12‐TMC)O₂]⁺ (12‐TMC = 1,4,7,10‐tetramethyl‐1,4,7,10‐tetraazacyclododecane) and [Ni(14‐TMC)O₂]⁺ (14‐TMC = 1,4,8,11‐tetramethyl‐1,4,8,11‐tetraazacyclotetradecane), has been inspected by means of difference‐dedicated configuration interaction calculations and a valence bond reading of the wavefunction. The system containing the 12‐membered macrocyclic ligand has been experimentally described as a side‐on nickel(III)‐peroxo complex, whereas the 14‐membered one has been characterized as an end‐on nickel(II)‐superoxide. Our results put in evidence the relationship between the steric effect of the macrocyclic ligand, the O₂ coordination mode and the charge transfer extent between the Ni center and the O₂ molecule. The 12‐membered macrocyclic ligand favors a side‐on coordination, a most efficient overlap between Ni 3d and O₂ π* orbitals and, consequently, a larger charge transfer from LNi fragment to O₂ molecule. The analysis of the ground‐state electronic structure shows an enhancement of the peroxide nature of the Ni? O₂ interaction for [Ni(12‐TMC)O₂]⁺, although a dominant superoxide character is found for both systems. © 2012 Wiley Periodicals, Inc.     

Two-body Reduced Density Matrix Reconstruction for Van der Waals Systems

A method for the calculation of the electronic energy of a correlated system is presented. This approach is based on the reconstruction of the total two-body reduced density matrix by doing separate configurations interaction calculations on fragments. The method has been tested on Van der Waals systems and has been implemented by considering restrictive N-representability conditions. It is shown that the computational strategy presented in this work can describe with good accuracy weak dispersion interactions, and considerably lowers the size-consistency error of a classical configuration interaction calculation.     

Substituent effects on noncovalent halogen/π interactions: Theoretical study

Noncovalent halogen/π interactions of FCl with substituted benzenes have been investigated using ab initio calculations. It was shown that the predicted maximum interaction energy gap between the substituted and unsubstituted systems amounts to 1.14 kcal/mol, and therefore substituents on benzene have a pronounced effect on the strength of halogen/π interactions. While the presence of electron‐donating groups (NH₂, CH₃, and OH) on benzene enhances the interaction energy appreciably, an opposite effect is observed for electron‐accepting groups (NO₂, CN, Br, Cl, and F). The large gain of the attraction by electron correlation illustrates that the stabilities of the systems considered arise primarily from the dispersion interaction. Beside the dispersion interaction, the charge‐transfer interaction also plays an important role in halogen/π interactions, as a charge density analysis suggested. To provide more insight into the nature of halogen/π interactions, topological analysis of the electron density distribution and properties of bond critical points were determined in terms of the atoms in molecules (AIM) theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A theoretical analysis of the explanation of the significant differences in antiferromagnetic interactions between homologous μ-alkoxo and acetate bridged dicopper(II) complexes: ab initio and semi-empirical calculations

A magnetostructural classification of dimmers, containing the Cu (μ-alkoxo) Cu core, based on data obtained from X-ray diffraction analysis reported in the literature has been performed. In these complexes, the local geometry around the copper ions is generally a square planar and each copper ion is surrounded by one N atom and three O atoms. The influence of the overlap interactions between the bridging ligands and the metal (Cu) d orbitals on the super-exchange coupling constant has been studied by means of ab initio Restricted Hatree–Fock molecular orbital calculations. The interaction between the magnetic d orbitals and highest occupied molecular orbitals of the acetate oxygens has been investigated in homologous μ-acetato-bridged dicopper(II) complexes which have significantly different −2J values (the energy separation between the spin-triplet and spin-singlet states). In order to determine the nature of the fronter orbitals, Extended Hückel molecular Orbital calculations are also reported. Ab initio restricted Hartree–Fock calculations have shown that the acetato bridge and the alkoxide bridge contribute to the magnetic interaction countercomplementarily to reduce antiferromagnetic interaction.     

Gas‐phase reactivity of 2‐hydroxy‐1,4‐naphthoquinones: a computational and mass spectrometry study of lapachol congeners

In order to understand the influence of alkyl side chains on the gas‐phase reactivity of 1,4‐naphthoquinone derivatives, some 2‐hydroxy‐1,4‐naphthoquinone derivatives have been prepared and studied by electrospray ionization tandem mass spectrometry in combination with computational quantum chemistry calculations. Protonation and deprotonation sites were suggested on the basis of gas‐phase basicity, proton affinity, gas‐phase acidity (ΔG_acid), atomic charges and frontier orbital analyses. The nature of the intramolecular interaction as well as of the hydrogen bond in the systems was investigated by the atoms‐in‐molecules theory and the natural bond orbital analysis. The results were compared with data published for lapachol (2‐hydroxy‐3‐(3‐methyl‐2‐butenyl)‐1,4‐naphthoquinone). For the protonated molecules, water elimination was verified to occur at lower proportion when compared with side chain elimination, as evidenced in earlier studies on lapachol. The side chain at position C(3) was found to play important roles in the fragmentation mechanisms of these compounds. Copyright © 2012 John Wiley & Sons, Ltd.     

Magnetic Coupling Constants of Self‐Assembled CuII [3×3] Grids: Alternative Spin Model from Theoretical Calculations

This paper reports a theoretical analysis of the electronic structure and magnetic properties of a ferromagnetic Cu^II [3×3] grid. A two‐step strategy, combining calculations on the whole grid and on binuclear fragments, has been employed to evaluate all the magnetic interactions in the grid. The calculations confirm an S=7/2 ground state, which is in accordance with the magnetisation versus field curve and the thermal dependence of the magnetic moment data. Only the first‐neighbour coupling terms present non‐negligible amplitudes, all of them in agreement with the structure and arrangement of the Cu 3d magnetic orbitals. The results indicate that the dominant interaction in the system is the antiferromagnetic coupling between the ring and the central Cu sites (J₃=J₄≈?31 cm^?1). In the ring two different interactions can be distinguished, J₁=4.6 cm^?1 and J₂=?0.1 cm^?1, in contrast to the single J model employed in the magnetic data fit. The calculated J values have been used to determine the energy level distribution of the Heisenberg magnetic states. The effective magnetic moment versus temperature plot resulting from this ab initio energy profile is in good agreement with the experimental curve and the fitting obtained with the simplified spin model, despite the differences between these two spin models. This study underlines the role that the theoretical evaluations of the coupling constants can play on the rationalisation of the magnetic properties of these complex polynuclear systems.     

Interpenetrating polar and nonpolar sublattices in intermetallics: the NaCd(2) structure

In the 1960s, Samson solved the structures of some of the most complicated intermetallic phases known, including those of NaCd(2), Mg(2)Al(3), and Cu(3)Cd(4) (each with over 1000 atoms per unit cell). Following remarkable earlier constructions by Samson and by Andersson, we use quantum-mechanical calculations as a guide to describing and understanding these structures. Our electronic Aufbau begins with the relatively simple Mg(17)Al(12) structure and works up to Samson's NaCd(2) structure. In both structures, a division of the sites into electron-rich and electron-poor (with respect to an average electron count) reveals MgCu(2)-type fragments. Between the interiors and exteriors of these fragments, a change in bonding character takes place-the interiors are more polar, the interfaces relatively nonpolar. This electronic situation is traced to the geometry of the interface sites; they lie simultaneously on electron-rich and electron-poor networks. The resulting polar and nonpolar sites in NaCd(2) are separated by a minimal surface, the D surface. The driving force for assuming this structure is electronic: NaCd(2) features an interpenetration of polar and nonpolar bonding regions. This sort of thinking can be applied to other structures.     

Deposition of the Spin Crossover FeII–Pyrazolylborate Complex on Au(111) Surface at the Molecular Level

The interaction at the molecular level of the spin-crossover (SCO) Fe^II((3,5-(CH₃)₂Pz)₃BH)₂ complex with the Au(111) surface is analyzed by means of rPBE periodic calculations. Our results show that the adsorption on the metallic surface enhances the transition energy, increasing the relative stability of the low spin (LS) state. The interaction indeed is spin-dependent, stronger for the low spin than the high spin (HS) state. The different strength of the Fe ligand field at low and high temperature manifests on the nature, spatial extension and relative energy of the states close to the Fermi level, with a larger metal–ligand hybridization in the LS state. This feature is of relevance for the differential adsorption of the LS and HS molecules, the spin-dependent conductance, and for the differences found in the corresponding STM images, correctly reproduced from the density of states provided by the rPBE calculations. It is expected that this spin dependence will be a general feature of the SCO molecule–substrate interaction, since it is rooted in the different ligand field of Fe site at low and high temperatures, a common hallmark of the Fe^II SCO complexes. Finally, the states involved in the LIESST phenomenon has been identified through NEVPT2 calculations on a model reaction path. A tentative pathway for the photoinduced LS→HS transition is proposed, that does not involve the intermediate triplet states, and nicely reproduces both the blue laser wavelength required for the activation, and the wavelength of the reverse HS → LS transition.     

Electronic and structural properties of the metalloporphyrin structural isomers: semiempirical AM1 and PM3 calculations

Semiempirical calculations using AM1 and PM3 have been performed on the zinc(II) and magnesium(II) complexes of nine structural isomers of tetrapyrrole macrocycles such as porphyrin, porphycene, corrphycene and hemiporphycene, N-confused porphyrin and other isomers that have not been synthesized. The optimized geometry and the bond parameters obtained compare favorably with results obtained from X-ray and spectral studies. Heats of formation, ionization potentials, HOMO-LUMO energy differences, dipole moments, and the splitting of HOMOs and LUMOs of the metal complexes of each of these isomers are also reported and compared with experimental results. The “four-orbital model” of Gouterman remains valid for the investigated structural isomers. The present study represents an unusually appropriate opportunity to study, via molecular orbital methods, the interaction between various metal ions, and the electronic and geometrical environment of the central cavity of the closely related isomeric macrocycles. The major outcome of this study is the verification of the expected differential behavior of metal ions employed in the present study as a sophisticated probe of cavity properties which also suggests that this procedure can be extended to other metal complexes. This study also serves as an interesting prototype for more elaborate ab initio calculations. However, such calculations on the presently investigated macrocyclic systems may have to be performed at a higher level than MP2 or DFT to account for the unusual delocalization, as suggested by a recent study by Schaefer and co-workers on delocalized [10]annulene (H.M. Sulzbach, H.F. Schaefer, W. Klopper and H.P. Luthi, J. Am. Chem. Soc., 118 (1996) 3519).     

Bond orders between molecular fragments

An extension of the Mayer bond order for the interaction between molecular fragments is presented. This approach allows the classical chemical concepts of bond order and valence to be utilised for fragments and the interactions between the fragments and symmetry-adapted linear combinations to be analysed. For high-symmetry systems, the approach allows the contribution from each irreducible representation to be assessed and provides a semiquantitative measure of the role of each bonding mode to interfragment interactions. The utility of this tool has been examined by a study of the bonding in symmetrical sandwich complexes. The validity of the frontier-orbital approach and the contributions from each frontier-orbital interaction can also be assessed within this model. As demonstrated by a study of a number of mixed-sandwich complexes, the model proves to be especially useful for low-symmetry systems in which separation of the sigma, pi and delta roles in bonding of the ligand is difficult to assess. The fragment bond order describes the interaction between preoptimized fragment orbitals and is independent of the charges that are placed on these fragments. Although the method allows the chemist to define fragments in any way they choose, most insight is gained by using the same frontier orbitals employed so successfully in perturbational molecular-orbital approaches. The results are free from the influence of the electron-counting method used to describe fragments, such as the rings and metals in sandwich complexes.     

How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

This study examines the accuracy of molecular dynamics-linear response (MD/LR) and Poisson–Boltzmann/solvent accessible surface (PB/SAS) calculations to predict relative binding affinities. A series of acetylcholinesterase (AChE) huprine inhibitors has been chosen as a test system owing to the availability of free-energy (thermodynamic integration) calculations. The results obtained with the MD/LR approach point out a clear relationship between the experimental affinity and the electrostatic interaction energy alone for a subset of huprines, but the suitability of the MD/LR approach to predict the binding affinity of the whole series of compounds is limited. On the other hand, PB/SAS calculations show a marked dependence on both the computational protocol and the nature of the inhibitor–enzyme complex. Received: 2 August 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000     

Rational Design of Electronically Labile Dinuclear Fe and Co complexes with 1,10-Phenanthroline-5,6-Diimine: A DFT study

A series of coordination compounds of redox-active 1,10-phenanthroline-5,6-diimine with Co^II bis-diketonates and Fe^II dihydrobis(pyrazolyl)borates has been computationally designed by means of density functional theory (DFT UB3LYP*/6-311++G(d,p)) calculations of their electronic structure, energy characteristics, and magnetic properties. Four types of complexes differing by the nature and position of the terminal metal-centered fragments have been considered. The performed systematic calculations have revealed the systems capable of undergoing thermally initiated spin-state switching rearrangements, including those governed by the synchronized mechanisms of spin crossover and valence tautomerism. The predicted magnetic characteristics allow one to consider the dinuclear cobalt complexes and heterometallic Co/Fe compounds with 1,10-phenanthroline-5,6-diimine as building blocks for molecular and quantum electronics devices. © 2019 Wiley Periodicals, Inc.     

Ab initio study of the complexes of halogen-containing molecules RX (X=Cl, Br, and I) and NH3: towards understanding the nature of halogen bonding and the electron-accepting propensities of covalently bonded halogen atoms

Ab initio calculations have been performed on a series of complexes formed between halogen-containing molecules and ammonia to gain a deeper insight into the nature of halogen bonding. It appears that the dihalogen molecules form the strongest halogen-bonded complexes with ammonia, followed by HOX; the charge-transfer-type contribution has been demonstrated to dominate the halogen bonding in these complexes. For the complexes involving carbon-bound halogen molecules, our calculations clearly indicate that electrostatic interactions are mainly responsible for their binding energies. Whereas the halogen-bond strength is significantly enhanced by progressive fluorine substitution, the substitution of a hydrogen atom by a methyl group in the CH(3)X...NH(3) complex weakened the halogen bonding. Moreover, remote substituent effects have also been noted in the complexes of halobenzenes with different para substituents. The influence of the hybridization state of the carbon atom bonded to the halogen atom has also been examined and the results reveal that halogen-bond strengths decrease in the order HC triple bond CX > H(2)C=CHX approximately O=CHX approximately C(6)H(5)X > CH(3)X. In addition, several excellent linear correlations have been established between the interaction energies and both the amount of charge transfer and the electrostatic potentials corresponding to an electron density of 0.002 au along the R-X axis; these correlations provide good models with which to evaluate the electron-accepting abilities of the covalently bonded halogen atoms. Finally, some positively charged halogen-bonded systems have been investigated and the effect of the charge has been discussed.     

Molecular orbital study for Na, Mg, and Al adsorption on the Si (111) surface

We investigated the interactions between the Si(111) surface and the Na, Mg, and Al atoms using cluster model calculations. Calculations were performed at levels of complete-active-space self-consistent-field (CASSCF) and multi-reference singly and doubly excited configuration interaction (MRSDCI) calculations using the model core potential method. Our calculations revealed that the most favorable sites of Na, Mg, and Al adsorption on Si(111) are on top (T₁), bridge (B₂), and 3-fold filled (T₄) sites, respectively. The nature of chemical bonds between these metal atoms and the dangling bonds of the surface Si atoms are found to be essentially covalent.     

Evaluation of magnetic terms in Cu4O4 cubane-like systems from selected configuration interaction calculations: a case study of polynuclear transition-metal systems

We present the evaluation of magnetic terms in a Cu(4)O(4) cubane-like system from truncated CI calculations, as a case study of polynuclear transition-metal complexes. We employ a new excitation selected configuration interaction (EXSCI) method based on the use of local orbitals. Taking advantage of the locality and then of the fact that the interactions vanish when the distance is large, the dimension of the CI is largely reduced. To the best of our knowledge these CI calculations are the largest one performed for polynuclear transition metal systems so far. The results show the presence of two leading ferromagnetic interactions between bridged Cu ions. Also the interactions between the unbridged Cu ions are ferromagnetic, but very weak, in contrast to the experimental data. The nature and amplitude of all the computed interactions are consistent with the relative orientation of the magnetic orbitals in the molecule, and correctly reproduce the susceptibility versus temperature curve. Our results indicate that it is possible to obtain similar fittings with sets of parameters representing different physical effects and put in evidence the drawbacks of the fitting based on oversimplified magnetic models. In this context, the presented computational strategy can be considered as a useful tool to help in the interpretation of the magnetic data and the validation of the magnetic interaction model in the polynuclear magnetic systems.