Computed Interaction Energies Research Articles

Transition Metal Cation−π Interactions: Complexes Formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ Binding with Benzene Molecules

A computational investigation of the structures and interaction energies of complexes formed by Fe2+, Co2+, Ni2+, Cu2+, and Zn2+ binding with benzene (Bz) molecules is performed employing high level ab initio quantum chemical methods, such as the second-order perturbation theory (MP2), coupled-cluster singles and doubles (CCSD), and coupled-cluster singles and doubles with perturbative triples [CCSD(T)] methods, along with the 6-311++G(2d,2p) and 6-311++G(d,p) basis sets. As far as we know, the present work is the first to study the structures and energetics of Bz-M2+ and Bz-M2+-Bz type complexes (M = Co, Ni, Cu, and Zn). Relativistic effects are also investigated via Douglas-Kroll-Hess second-order scalar relativistic computations for the complexes considered. Our results demonstrate that there are strong bindings between transition metal cations and benzene molecules. The computed interaction energies, including relativistic energy corrections, for the Bz-M2+ type complexes at the CCSD(T)/6-311++G(2d,2p) level are -131.9 (Bz-Fe2+), -172.6 (Bz-Co2+), -189.8 (Bz-Ni2+), -181.1 (Bz-Cu2+), and -158.2 (Bz-Zn2+) kcal mol-1. Similarly, interaction energies for the Bz-M2+-Bz type complexes at the CCSD(T)/6-311++G(d,p) level are -206.4 (Bz-Fe2+-Bz), -213.4 (Bz-Co2+-Bz), -249.7 (Bz-Ni2+-Bz), -258.6 (Bz-Cu2+-Bz), and -235.2 (Bz-Zn2+-Bz) kcal mol-1. Further, our results also demonstrate that the relativistic effects are very important in accurate computations of interaction energies. The predicted relativistic energy corrections to interaction energies, using the ωB97X-D functional, are between -1.9 and -7.7 kcal mol-1. The transition metal cation-π interactions investigated in this study prove significantly larger binding energies compared to arbitrary π-π interactions and main group cation-π interactions. We believe that the present study may open new avenues in cation-π interactions.

Inhibition activities of catechol diether based non-nucleoside inhibitors against the HIV reverse transcriptase variants: Insights from molecular docking and ONIOM calculations

The therapeutic effectiveness of the catechol diether analogs against both the wild-type and drug-resistant reverse transcriptase (RT) mutants of HIV strains are investigated by performing molecular docking and hybrid ONIOM calculations. The docking protocol has been used to predict the binding modes of the non-nucleoside inhibitors inside the active site cavity of the viral enzymes. For each enzyme-inhibitor adduct, the predicted docked poses are assessed by employing different scoring function based programs. However, the docking protocol fails to explain satisfactorily the antiviral activities of the drug molecules. Two-layered ONIOM calculations have been carried out to compute the relative binding affinities of the catechol diether derivatives to the binding pockets of RT variants. The binding efficacies of the inhibitors are significantly suppressed by the Y181C and K103N mutations, as revealed by the computed interaction energies at the ONIOM [B3LYP/6-31G(d,p):PM6] level of theory. Deformation energies for each bound ligand conformer are also estimated. The nature of interactions between the drug molecules and the active site residues are analyzed from the reduced density gradient (RDG) isosurfaces. The simulated ECD spectra support the conformational adaption upon inhibitor binding in the binding pockets of HIV strains.

Performance of CuII -, PbII -, and HgII -Exchanged Mordenite in the Adsorption of I2 , ICH3 , H2 O, CO, ClCH3 , and Cl2 : A Density Functional Study.

Periodic dispersion-corrected DFT is used to investigate the adsorption of I2 and ICH3 , which may be released during a severe nuclear accident, for three divalent cation (Cu2+ , Pb2+ and Hg2+ )-exchanged mordenites with an Si/Al ratio of 23. Gases such as H2 O, CO, ClCH3 , and Cl2 present in the containment atmosphere can inhibit the selective adsorption of iodine species. To identify the most promising adsorbents, a systematic study is performed in which all the possible cationic sites in the main channel of the mordenite structure are considered. For the energetically most stable sites, the divalent cation is located in the small rings (five- or six-membered) containing two Al atoms, while in the energetically less stable configurations, the two Al atoms are far apart (>7 Å) and the cation is close to only one Al atom. Upon adsorption of the various molecules, the coordination number of the cation decreases with increasing interaction energy, as the molecules can attract the divalent cations from the framework. Finally, the computed interaction energies show that Hg-mordenite (MOR) could be a suitable material for selective adsorption of volatile iodine species, contrary to Cu-MOR and Pb-MOR.

Parametrization of Non-covalent Interactions for Transition State Interrogation Applied to Asymmetric Catalysis.

The use of computed interaction energies and distances as parameters in multivariate correlations is introduced for postulating non-covalent interactions. This new class of descriptors affords multivariate correlations for two diverse catalytic systems with unique non-covalent interactions at the heart of each process. The presented methodology is validated by directly connecting the non-covalent interactions defined through empirical data set analyses to the computationally derived transition states.

In silico Meta-Analysis of Circulatory microRNAs in Prostate Cancer

Circulatory microRNAs (miRNAs) have emerged as a new class of non coding RNA molecules which regulate many crucial molecular and biological processes. We have aimed to shed light on the roles of circulatory miRNAs in Prostate Cancer (PCa) using an integrative in silico bioinformatics approach. We have described a new protocol for target prediction and functional analysis which was applied to 40 highly differentially dysregulatedcirculatory miRNAs in PCa. This framework comprises: (i) evidence of involvement of these circulatory miRNAs from previous literature and microarray analysis (ii) overlap of prediction results by target prediction tools, including miRTarBase, miRDB, DIANA- microT 4.0 and TargetScan (combining computational learning, alignment, interaction energy and statistical tests for minimization of false positives), (iii) gene ontology (GO) along with pathway enrichment analysis of the miRNA targets and their pathways and (iv) linking these pathways to oncogenesis and cancer hallmarks. More than 200 target genes and 40 regulatory pathways were retrieved and analysed which was followed by associating their roles with cancer hallmark processes. Wnt signalling, Cell cycle, MAPK signalling, Cadherin signalling, Integrin signalling and Ras pathways were some of the identified regulatory pathways during bioinformatics analysis. These signalling and developmental pathways crosstalk and regulate stem cell renewal thus indicating a definite role of circulatory miRNAs in PCa development. Our study identified miR-181, miR-9, Let-7 family, miR-26b circulatory miRNAs, to be contributing majorly in the oncogenic pathways, thus proposing their role as potential biomarkers in PCa initiation and progression.

Experimental and theoretical analysis of substituent effect on charge transfer complexes of iodine and some alkylbenzenes in n-hexane solution at 303 K

Abstract The charge transfer (CT) interactions in n-hexane solutions containing iodine (acceptor) and aromatic compounds, benzene (BEN), toluene (TOL), o -xylene (OXYL), m -xylene (MXYL) and mesitylene (MESI) were investigated by ultrasonic, UV-Visible spectroscopic methods and DFT analysis. The trend in acoustical and excess properties with molar concentration in these systems established the existence of strong solute–solute interaction and formation of CT complex between iodine and the five aromatic compounds. Computed interaction energy values in the present investigation confirmed the formation of CT complex in these systems. Both the experimental methods and theoretical investigation of these systems indicated that tendency for formation of CT complex increases with increase in the number of methyl substituent in the aromatic ring. Our computed results are in good agreement with the experimental observations.

Revealing the physical nature and the strength of charge-inverted hydrogen bonds by SAPT(DFT), MP2, SCS-MP2, MP2C, and CCSD(T) methods

The physical nature of charge-inverted hydrogen bonds in H3 XH ⋯YH3 (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)-based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS-MP2, MP2C, and CCSD(T) methods utilizing dimer-centered aug-cc-pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge-inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: EintSAPT<EintSCS-MP2≤EintMP2C<EintMP2≈EintCCSD(T). It is confirmed that the aug-cc-pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole-ζ quality. Considerably large binding energies suggest potential usefulness of charge-inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ- and π-hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge-inverted hydrogen bond would become the first described case of a hydride-triel bond. © 2017 Wiley Periodicals, Inc.

Hydrogen Bonding between Metal-Ion Complexes and Noncoordinated Water: Electrostatic Potentials and Interaction Energies.

The hydrogen bonding of noncoordinated water molecules to each other and to water molecules that are coordinated to metal-ion complexes has been investigated by means of a search of the Cambridge Structural Database (CSD) and through quantum chemical calculations. Tetrahedral and octahedral complexes that were both charged and neutral were studied. A general conclusion is that hydrogen bonds between noncoordinated water and coordinated water are much stronger than those between noncoordinated waters, whereas hydrogen bonds of water molecule in tetrahedral complexes are stronger than in octahedral complexes. We examined the possibility of correlating the computed interaction energies with the most positive electrostatic potentials on the interacting hydrogen atoms prior to interaction and obtained very good correlation. This study illustrates the fact that electrostatic potentials computed for ground-state molecules, prior to interaction, can provide considerable insight into the interactions.

MP2 Study of Physisorption of Molecular Hydrogen onto Defective Nanotubes: Cooperative Effect in Stone-Wales Defects.

We use large-scale MP2 calculations to investigate the physisorption of molecular hydrogen on (9,0) defective carbon nanotubes (CNTs) of C72H18. These large (supra)molecular systems are typically studied using conventional DFT methods, which do not describe well the van der Waals interactions responsible for this process. Here we use CCSD(T)-calibrated MP2 calculations to estimate binding energies by considering four defective structures (hydrogenated divacancy, octagon-pentagon, and two Stone-Wales defects). The largest physisorption energies for the nondefective CNT are for configurations in which H2 points toward the center of one ring. The computed interaction energies for defect-free CNT are in the range 5.7 to 5.9 kJ/mol, in good agreement with the experimental value of 5.98 kJ/mol. The defects introduced in the (9,0)-CNT increase the surface area of the nanotube, such that the largest surface in found in the 55-77 Stone-Wales defective CNT that furthermore is the most aromatic. Only that defect enlarges the physisorption binding energy, which can become >25% larger. Moreover, a cooperative effect in the adsorption of H2 not appearing in the regular structure is found.

On the formation of beryllium bonds where radicals act as electron donors

The complexes between BeX2 (X = F, H) with CH3, CH2CH3, CH(CH3)2 and C(CH3)3 radicals have been characterized by using the MP2 and CCSD(T) methods and AIM procedure. The formation of these complexes is found to originate from the interaction between the positively charged Be atom and the unpaired electron of the radicals, and this interaction is closed shell in essence. During complexation with radicals, all the BeX2 molecules feature redshifted X–Be–X antisymmetric stretching vibrations, according well with the lengthening of Be–X bonds. According to the computed interaction energies, methyl substitution imposes a positive effect on the complex formation. Energy decomposition analysis indicate that the stability of the topic complexes mainly comes from the attractive electrostatic and polarization terms, which is similar to the case of π-beryllium bonds. By comparisons with some related systems, it can be concluded that the bond strength increases in the order single-electron hydrogen bond < single-electron sodium bond < single-electron lithium bond < single-electron beryllium bond ≈ π-beryllium bond.

Density Functional Theory Computations for Design of Salicylaldoxime Derivatives as Selective Reagents in Solvent Extraction of Copper

We have performed density functional theory computations to study interactions of salicylaldoxime (SALO) and its derivatives possessing appropriate alkyl group substitution in the main chain (CM-SALO) or side chain (CS-SALO) with copper, zinc and lead divalent ions. The objective of this study was to understand the underlying interaction mechanisms so as to exploit this knowledge in the design and development of selective reagents for solvent extraction. All computations were performed using plane wave ultrasoft pseudopotentials and Perdew–Burke–Ernzerhof generalized gradient approximation as implemented in the Plane Wave Self consistent field code. The relative order of selectivity, as per the computed interaction energies, was found to be: Cu > Zn > Pb. CM-SALO derivatives exhibited stronger interactions as compared to the CS-SALO derivatives. Our findings were consistent with our experimental results reported earlier and were explained by highest occupied molecular orbital–lowest unoccupied molecular orbital and Lowdin charge analyses.

Intuitive and counterintuitive noncovalent interactions of aromatic π regions with the hydrogen and the nitrogen of HCN

We have investigated intuitive and counterintuitive complex formation between eight aromatic molecules and HCN. In four of the former, the π regions had negative electrostatic potentials; in the other four, the π regions had positive potentials. Each aromatic molecule was allowed to interact through its π region with both the hydrogen (positive potential) of HCN and also the nitrogen (negative potential). In eight cases, therefore, interaction was intuitively favorable (positive/negative) while in the other eight, attractive interaction would be counterintuitive on the basis of the ground state electrostatic potentials (positive/positive or negative/negative). The intuitive interactions all led to bound complexes, and five of the counterintuitive did as well. The Hellmann–Feynman theorem was invoked to help explain the formation of the five counterintuitive complexes in terms of polarization/dispersion. Very good correlations were obtained, for the intuitive and also the counterintuitive complexes, between the computed interaction energies and values predicted solely on the basis of the most positive and the most negative electrostatic potentials in the π regions and on the HCN.

Quantum-chemical study on stacking interactions between bioactive polyphenols (trans-resveratrol, trans-piceatannol) and ribonucleosides. Insight into minimum energy geometries of π–π stacked systems

The minimum energy geometries and one-electron properties of the polyphenols (trans-resveratrol and trans-piceatannol) as well as their π–π stacking interactions with ribonucleosides were investigated by means of the M062X/6–311+G(d,p) level of quantum theory in vacuum and water medium. Within the theory level applied, the polyphenols studied exhibit large polarizability. This study presents computed interaction energies of selected complexes ranging from 17.6 to 26.9kcalmol−1 in vacuum. It has been observed that the stability of the chemical systems decreases in water medium, described by Conductor-like Polarizable Continuum Model (CPCM). For the first time we have predicted that trans-piceatannol binds strongly with ribonucleosides. A complex of trans-piceatannol with adenosine has been found to be the most energetically stable in water medium from among the systems considered within the applied quantum method. All systems studied have been shown to bear π–π stacking interactions and to be bound strongly in the media studied. It is concluded that π–π stacking interactions between ribonucleosides and polyphenols studied play a very important role in binding polyphenols in the complexes investigated. The results reveal that for trans-resveratrol–adenosine (vacuum and water medium) and trans-resveratrol–guanosine (vacuum and water medium), the local energy minima are sandwich structures, and the local energy minima for the other structures are parallel-displaced. This study provides significant insight into the stacked geometries of potential polyphenolic intercalators and can allow other scientist to design new antiviral drugs, basing on a mechanism that hadn’t been used in rational antiviral drug design.

Inherent carbonaceous impurities on arc-discharge multiwalled carbon nanotubes and their implications for nanoscale interfaces

This paper presents evidence that strongly adhered carbonaceous surface impurities, intrinsic impurities that accompany multiwall carbon nanotubes (MWCNTs) synthesized by arc-discharge, are a component that cannot be ignored in experiments involving single nanotubes and their interfaces with a second surface. At the interface that forms between a carbon nanotube and a graphitic surface, these impurities can significantly alter the adhesion properties of the underlying nanotube and can cause over 30% scatter in computed interaction energies, similar in magnitude to the scatter reported in experimental measurements involving individual CNTs. Also presented is high-resolution TEM evidence that commonly used purification techniques that are effective at removing larger impurity particles from as-produced arc-discharge MWCNT samples do not remove these strongly adhered carbonaceous surface impurities.

Global ab initio potential energy surface for the O2((3)Σ(g)(-)) + N2((1)Σ(g)(-)) interaction. Applications to the collisional, spectroscopic, and thermodynamic properties of the complex.

A detailed characterization of the interaction between the most abundant molecules in air is important for the understanding of a variety of phenomena in atmospherical science. A completely ab initio global potential energy surface (PES) for the O2((3)Σg(–)) + N2((1)Σg(+)) interaction is reported for the first time. It has been obtained with the symmetry-adapted perturbation theory utilizing a density functional description of monomers [SAPT(DFT)] extended to treat the interaction involving high-spin open-shell complexes. The computed interaction energies of the complex are in a good agreement with those obtained by using the spin-restricted coupled cluster methodology with singles, doubles, and noniterative triple excitations [RCCSD(T)]. A spherical harmonics expansion of the interaction potential containing a large number of terms due to the anisotropy of the interaction has been built from the ab initio data. The expansion coefficients, which are functions of the intermolecular distance, are matched in the long-range with the analytical functions based on the recent ab initio calculations of the electric properties of the monomers [M. Bartolomei et al. J. Comput. Chem. 2011, 32, 279]. The PES is tested against the second virial coefficient B(T) data and the integral cross sections measured with rotationally hot effusive beams, leading in both cases to a very good agreement. The lowest lying states of the complex have been computed and relevant spectroscopic features of the interacting complex are reported. A comparison with a previous experimentally derived PES is also provided.

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers.

Computational spectroscopy techniques have become in the last few years an effective means to analyze and assign infrared (IR) spectra of molecular systems of increasing dimensions and in different environments. However, transition from compilation of harmonic data to fully anharmonic simulations of spectra is still underway. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed at quantitative reproduction of the spectra of nucleic acid base complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work we have chosen two popular and inexpensive approaches to model dispersion interactions, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

OptZyme: Computational Enzyme Redesign Using Transition State Analogues

OptZyme is a new computational procedure for designing improved enzymatic activity (i.e., kcat or kcat/KM) with a novel substrate. The key concept is to use transition state analogue compounds, which are known for many reactions, as proxies for the typically unknown transition state structures. Mutations that minimize the interaction energy of the enzyme with its transition state analogue, rather than with its substrate, are identified that lower the transition state formation energy barrier. Using Escherichia coli β-glucuronidase as a benchmark system, we confirm that KM correlates (R2 = 0.960) with the computed interaction energy between the enzyme and the para-nitrophenyl- β, D-glucuronide substrate, kcat/KM correlates (R2 = 0.864) with the interaction energy of the transition state analogue, 1,5-glucarolactone, and kcat correlates (R2 = 0.854) with a weighted combination of interaction energies with the substrate and transition state analogue. OptZyme is subsequently used to identify mutants with improved KM, kcat, and kcat/KM for a new substrate, para-nitrophenyl- β, D-galactoside. Differences between the three libraries reveal structural differences that underpin improving KM, kcat, or kcat/KM. Mutants predicted to enhance the activity for para-nitrophenyl- β, D-galactoside directly or indirectly create hydrogen bonds with the altered sugar ring conformation or its substituents, namely H162S, L361G, W549R, and N550S.

H Atom Adsorption on a Silicate Surface: The (010) Surface of Forsterite

We present a first-principles computational study of the interaction of an H atom with the (010) surface of forsterite (Mg2SiO4). Periodic DFT-GGA calculations (PBE) are carried out using the SIESTA code with core pseudopotentials and TZP localized basis sets. Potential energy curves are determined for the approach of the H atom toward different sites of the surface: atop, near, or in between the O, Mg, and Si atoms. An outer adsorption well is found for all investigated sites; it is deepest (162 meV) at a so-called “displaced Mg–O bridge” position. The binding at this well is of the “weak chemisorption”/“strong physisorption” type. An inner stronger chemisorption well (670 meV deep) exists exclusively near an O site but not strictly atop. Depending on the path, we find activation barriers (25–170 meV high) against chemisorption, the lowest of these occurs for the top O site. General trends of the computed interaction energies qualitatively agree with the QM/MM results of Goumans et al. [Mon. Not. R. Astr...

Investigation of CHBrF2 adsorbed on TiO2 through IR spectroscopy and DFT calculations

The adsorption of bromodifluoromethane (CHBrF2) on TiO2 has been investigated through IR spectroscopy for the first time. The spectrum of the adsorbed molecule suggests that the compound binds weakly to the surface site preferably through the Br atom. DFT/B3LYP calculations on the possible adsorption structures have been carried out on the anatase (101) surface simulating the interaction between the five-fold coordinated titanium ion and one of the halogen atoms. In the case of the interaction through the Br atom, the adsorption has been modeled both in presence and in absence of H-bond between the adsorbate and the substrate and only in the first case the calculated binding and interaction energies indicate a favorable adsorption. An attraction between the molecule and the surface in case of adsorption through the F atom is found possible according to the computed interaction energies. The comparison between the observed and calculated vibrational frequencies confirms that the adsorption involves the Br and H atoms. Moreover, it suggests that also the interaction through the F and H atoms is possible. The work shows the importance of the simulation of the possible adsorbate–substrate structures in order to better interpret the experimental data.

Hydrogenation and Fluorination of Graphene Models: Analysis via the Average Local Ionization Energy

We have investigated the use of the average local ionization energy, I[combining overline](S)(r), as a means for rapidly predicting the relative reactivities of different sites on two model graphene surfaces toward the successive addition of one, two, and three hydrogen or fluorine atoms. The I[combining overline](S)(r) results were compared with directly computed interaction energies, at the B3LYP/6-311G(d,p) level. I[combining overline](S)(r) correctly predicts that the edges of graphene sheets are more reactive than the interior portions. It shows that added hydrogens activate the adjoining (ortho) sites and deactivate those that are separated by one site (meta). Overall, I[combining overline](S)(r) is effective for rapidly (single calculations) estimating the relative site reactivities of these large systems, although it reflects only the system prior to an interaction and cannot take into account postinteraction factors, e.g., structural distortion.