Contribution To Interaction Energy Research Articles

КОНФОРМАЦИОННЫЕ СВОЙСТВА И ЭЛЕКТРОННАЯ СТРУКТУРА ПРОТИВООПУХОЛЕВОГО АГЕНТА TYR-SER-LEU

Molecular modeling methods were used to study the features of the spatial and electronic structure of the antitumor tripeptide YSL (Tyr-Ser-Leu), developed by Chinese scientists. The conformational analysis of the molecule revealed a limited set of its energetically preferable conformational states in a certain range of relative energy. The nature of the forces stabilizing the low-energy conformations of the tripeptide molecule was determined. As a result of the study, the energetically preferable ranges of dihedral angles, the energy contributions of interresidual interactions and hydrogen bonds, as well as the mutual arrangement of residues and their side chains in low-energy conformations of the tripeptide were also determined. Using the methods of molecular mechanics, the energy contributions of intramolecular interactions in low-energy conformational states of the molecule were obtained. Based on quantum-chemical calculations, the distribution of electron density and the values of dipole moments of the most optimal spatial structures of the YSL tripeptide molecule were determined. The reactivity of the tripeptide was also studied by quantum chemical calculations based on the obtained electronic characteristics of each low-energy conformation of the molecule. Using the calculated coordinates of the atoms of the energetically preferable structures of the molecule, their molecular models were built, the comparison of which makes it possible to identify the structural criteria necessary to create a drug suitable for clinical use.

An atomic surface site interaction point description of non-covalent interactions.

Molecular electrostatic potential surfaces (MEPS) calculated using density functional theory have been used to develop a simplified description of the non-covalent interaction properties of organic molecules. The Atomic Interaction Point (AIP) model introduced here represents an evolution of the Surface Site Interaction Point (SSIP) model described previously, in which a molecule is represented by a discrete set of interaction points that define sites of interaction with other molecules. The interaction sites are described by interaction parameters that are equivalent to the experimentally determined H-bond donor and acceptor parameters α and β. By using high electron density MEPS that lie inside the van der Waals surface, it is possible to obtain accurate interaction parameters and locations for polar sites (s-holes, H-bond donors and acceptors), which are identified as local maxima and minima on the MEPS. For non-polar sites that represent π-systems and halogens, an approach based on molecular orbitals was used to assign the locations of the AIPs, and the interaction parameters were obtained using a lower electron density MEPS that lies close to the van der Waals surface. The AIP descriptions can be implemented directly in the Surface Site Interaction Point Model for Liquids at Equilibrium (SSIMPLE) to calculate solvation free energies, and the free energy of transfer of 1504 compounds from n-hexadecane to water was predicted with a root mean square error of 5 kJ mol-1. AIPs also provide a useful tool for mapping non-covalent interactions in intermolecular complexes, and examples are provided showing how X-ray crystal structures can be converted into AIP interaction maps that allow quantification of the free energy contributions of both polar and non-polar interactions to the stabilities of complexes in solution.

'SAXS-osmometer' method provides measurement of DNA pressure in viral capsids and delivers an empirical equation of state.

We present a novel method that provides a measurement of DNA pressure in viral capsids using small angle X-ray scattering (SAXS). This method, unlike our previous assay, does not require triggering genome release with a viral receptor. Thus, it can be used to determine the existence of a pressurized genome state in a wide range of virus systems, even if the receptor is not known, leading to a better understanding of the processes of viral genome uncoating and encapsidation in the course of infection. Furthermore, by measuring DNA pressure for a collection of bacteriophages with varying DNA packing densities, we derived an empirical equation of state (EOS) that accurately predicts the relation between the capsid pressure and the packaged DNA density and includes the contribution of both DNA-DNA interaction energy and DNA bending stress to the total DNA pressure. We believe that our SAXS-osmometer method and the EOS, combined, provide the necessary tools to investigate physico-chemical properties of confined DNA condensates and mechanisms of infection, and may also provide essential data for the design of viral vectors in gene therapy applications and development of antivirals that target the pressurized genome state.

Analytical Solution to the Flory-Huggins Model.

A self-consistent analytical solution for binodal concentrations of the two-component Flory–Huggins phase separation model is derived. We show that this form extends the validity of the Ginzburg–Landau expansion away from the critical point to cover the whole phase space. Furthermore, this analytical solution reveals an exponential scaling law of the dilute phase binodal concentration as a function of the interaction strength and chain length. We demonstrate explicitly the power of this approach by fitting experimental protein liquid–liquid phase separation boundaries to determine the effective chain length and solute–solvent interaction energies. Moreover, we demonstrate that this strategy allows us to resolve differences in interaction energy contributions of individual amino acids. This analytical framework can serve as a new way to decode the protein sequence grammar for liquid–liquid phase separation.

Contribution of extracellular polymeric substances fractions to the adsorption of silver nanoparticles by activated sludge

The extracellular polymeric substances (EPS) from activated sludge played significant roles in the removal of nanoparticles from wastewater. A series of batch experiments were carried out to determine the adsorption mechanism of three nano-Ag by activated sludge, as well as the contributions of EPS fractions including dissolved EPS (DEPS), loosely bound EPS (LB-EPS) and tightly bound EPS (TB-EPS). The results demonstrated that the adsorption of nano-Ag by sludge biomass agreed with pseudo-second-order kinetic reaction model and Freundlich isotherm model. About 26.0–41.2% of nano-Ag was trapped by the bound EPS (BEPS) matrix of activated sludge (especially LB-EPS) and 42.5–52.6% of them was adsorbed onto the inner cells after the adsorption. Moreover, the interaction energy contributions of EPS fractions followed the order of EDE > 0 > ETB > ELB, suggesting DEPS in wastewater went against the removal of nano-Ag due to steric repulsion while LB-EPS and TB-EPS were positive to nano-Ag adsorption by modifying biomass surface and providing extensive binding sites. Besides, EPS fractions played significant roles in the adsorption of nano-Ag with low initial concentrations but had limited effect at high concentrations. Overall, this study investigated the effect of EPS fractions on the adsorption behaviors of nano-Ag by activated sludge biomass, which is meaningful to understand the removal mechanism of nanoparticles in sewage and the potential role of EPS fractions.

Three-body potential energy surface for para-hydrogen.

We present a 3D isotropic ab initio three-body (para-H2)3 interaction potential energy surface (PES). The electronic structure calculations are carried out at the correlated coupled-cluster theory level, with single, double, and perturbative triple excitations. The calculations use an augmented correlation-consistent triple zeta basis set and a supplementary midbond function. We construct the PES using the reproducing-kernel Hilbert space toolkit [O. T. Unke and M. Meuwly, J. Chem. Inf. Model. 57, 1923 (2017)] with phenomenological and empirical adjustments to account for short-range and long-range behaviors. The (para-H2)3 interaction energies deviate drastically from the Axilrod-Teller-Muto (ATM) potential at short intermolecular separations. We find that the configuration of three para-H2 molecules at the corners of an equilateral triangle is responsible for the majority of the (para-H2)3 interaction energy contribution in a hexagonal-close-packed lattice. In cases where two para-H2 molecules are close to one another while the third is far away, the (para-H2)3 interaction PES takes the form of a modified version of the ATM potential. We expect the combination of this PES together with a first-principles para-H2-para-H2 adiabatic hindered rotor potential to outperform a widely used effective pair potential for condensed many-body systems of para-H2.

Crystal engineering of a co-crystal of antipyrine and 2-chlorobenzoic acid: relative energetic contributions based on multipolar refinement

The growth and stability of a new 1 : 1 antipyrene–dichlorobenzoic acid cocrystal system has been analyzed in terms of electron density analysis and electrostatic interaction energy contributions.

Resonance-Assisted Hydrogen Bond-Revisiting the Original Concept in the Context of Its Criticism in the Literature.

In the presented research, we address the original concept of resonance-assisted hydrogen bonding (RAHB) by means of the many-body interaction approach and electron density delocalization analysis. The investigated molecular patterns of RAHBs are open chains consisting of two to six molecules in which the intermolecular hydrogen bond stabilizes the complex. Non-RAHB counterparts are considered to be reference systems. The results show the influence of the neighbour monomers on the unsaturated chains in terms of the many-body interaction energy contribution. Exploring the relation between the energy parameters and the growing number of molecules in the chain, we give an explicit extrapolation of the interaction energy and its components in the infinite chain. Electron delocalization within chain motifs has been analysed from three different points of view: three-body delocalization between C=C-C, two-body hydrogen bond delocalization indices and also between fragments (monomers). A many-body contribution to the interaction energy as well as electron density helps to establish the assistance of resonance in the strength of hydrogen bonds upon the formation of the present molecular chains. The direct relation between interaction energy and delocalization supports the original concept, and refutes some of the criticisms of the RAHB idea.

Structures and interactions of insulin-like peptides from cone snail venom.

The venomous insulin-like peptides released by certain cone snails stimulate hypoglycemic shock to immobilize fish and catch the prey. Compared to human insulin (hIns), the cone snail insulins (Con-Ins) are typically monomeric and shorter in sequence, yet they exhibit moderate hIns-like biological activity. We have modeled six variants of Con-Ins (G3, K1, K2, T1A, T1B, and T2) and carried out explicit-solvent molecular dynamics (MD) simulations of eight types of insulins, two with known structures (hIns and Con-Ins-G1) and six Con-Ins with modeled structures, to characterize key residues of each insulin that interact with the truncated human insulin receptor (μIR). We show that each insulin/μIR complex is stable during explicit-solvent MD simulations and hIns interactions indicate the highest affinity for the "site 1" of IR. The residue contact maps reveal that each insulin preferably interacts with the αCT peptide than the L1 domain of IR. Through analysis of the average nonbonded interaction energy contribution of every residue of each insulin for the μIR, we probe the residues establishing favorable interactions with the receptor. We compared the interaction energy of each residue of every Con-Ins to the μIR and observed that γ-carboxylated glutamate (Gla), His, Thr, Tyr, Tyr/His, and Asn in Con-Ins are favorable substitutions for GluA4, AsnA21, ValB12, LeuB15, GlyB20, and ArgB22 in hIns, respectively. The identified insulin analogs, although lacking the last eight residues of the B-chain of hIns, bind strongly to μIR. Our findings are potentially useful in designing potent fast-acting therapeutic insulin.

Thermodynamic and structural description of relative solubility of the flavonoid rutin by DFT calculations and molecular dynamics simulations

Understanding the solubility of flavonoids is of relevance in view of the broad application such as antioxidant and antitumor agents. The solubility of flavonoid rutin has been experimentally investigated in a homologous series of alcohols, acetone, n-heptane and water solvents. In this work theoretical evaluation of Gibbs free energy of solvation was performed at the Density Functional Theory (DFT) and Molecular Dynamics (MD) levels, with the ωB97x-D functional and multistate Bennett acceptance ratio (MBAR) method, respectively. The degree of solubility of a given solute among various solvents is dictated by solute-solvent interactions, which may be represented by the solvation energy. Our calculated relative energy values due to solvent effects, using quantum chemical methods (PCM and SMD solvent models) do not follow strictly the observed solubility trend. However, the PCM model including solute-solvent dispersion interaction, solute-solvent repulsion interaction and solute cavitation energy contribution to the total energy (named DIS,REP,CAV) yielded an overall agreement with experimental solubility profile, with exception of ethanol solvent. A similar satisfactory accordance with experiment was found for MBresults, with a discrepancy also found for 1-butanol, which deserve further investigation. Analysis of spatial and radial distribution functions (SDF and RDF) for pure solvents and the analysis of the contributions of vdW and electrostatic terms for the total free energy reveal that a balance between dispersive and electrostatic interactions between the rutin and the solvent is necessary to solubilize the flavonoid, which corroborates with the values of these energy contributions to the solvation-free energy calculated by the MBAR method. The use of explicit solvent molecules in DFT calculations is precluded due to the size, flexibility, and many sites for solvent interactions of rutin molecule. Our results indicate that in general DFT-PCM (DIS,REP,CAV) and MBAR levels of calculations can satisfactorily predict the solvation free energy and solubility trend for flavonoid rutin along a series of solvents, and also provide a reasonable estimate of relative solubilities of other flavonoids, information that can be relevant for further molecular modeling studies.

Theoretical insight into the hybridization effect of donor and acceptor atoms on the cooperativity of C-H···N hydrogen bonds.

In the present work, the influence of hybridization on cooperativity between C-H···N hydrogen bonds is theoretically investigated. Here, C2H6, C2H4, and C2H2 are considered as hydrogen bonding donor while NH3, N2H4, N2H2, and N2 act as the hydrogen bonding acceptor. The calculations are performed at MP2/aug-cc-pVTZ level. It is observed that the stability of systems is amplified as C(sp) > C(sp2) > C(sp3) and also N(sp3) > N(sp2) > N(sp). The role of interaction and deformation energies on the stability of the systems is examined. The results indicate the contribution of interaction energy is dominant in all complexes. The strength of C-H···N hydrogen bond is estimated using interaction energy. In agreement with cooperative energies, the C-H···N hydrogen bond is respectively weakened/strengthened in the triads containing C(sp) and C(sp2)/C(sp3) where two hydrogen bonds coexist. On the other hand, the C-H···N hydrogen bond is strengthened in the ternary systems including N(sp3) and N(sp2) while an opposite behavior is obtained in the triad having N(sp).

B3LYP, M06 and B3PW91 DFT assignment of nd8 metal-bis-(N-heterocyclic carbene) complexes.

This paper is focused on the examination of the bonding properties of a series of [M(NHC)2X2] (M = nd8 transition metal; X = Cl, Br and I) complexes in normal, abnormal and mixed C∩C coordination modes. Structures have been optimised in gas phase using B3LYP, M06 and P3BW91 functionals. Two basis sets have been used: the LanL2DZ and a mixed basis set (LanL2DZ for nd8 transition metals as well as halogen atoms and 6-311+G(d,p) for other atoms). Results obtained indicate that the B3PW91 bond distances are closer to experimental data. The complexation energies obtained for each binding mode increase in the order: Ni2+ < Pd2+ < Pt2+, independently of the halogen atom adopted. From the Quantum Theory of Atoms in Molecule (QTAIM) approach, the instability has been found to follow this trend: M - X < M - C. The analysis of metal-ligand interactions using the natural bond orbital (NBO) revealed that the strongest metal-ligand interactions are observed in the normal binding mode. The NCH → MX2 donation terms were found to be interestingly predominant compared with back donation ones in the complexes studied, except in Pt chloride ones. The contribution of electrostatic interaction energy between the above fragments (∆Eelstat term) is in the range 57.48-63.95% traducing the fact that the interactions are mostly electrostatic. Graphical abstract.

The Antifriction Properties of Amorphous Poly(Arylene Ether Ketone) Copolymers with a Low Content of Cardo Groups

The causes of an abrupt decrease in the wear and in the friction coefficient from 0.6 to 0.24 for poly(arylene ether ketone) copolymers containing 10, 15, and 25 mol % of cardo bisphenol moieties in the main chain have been investigated. The presence of cardo groups in the copolymers promotes an increase in the microhardness from 12 to 22 kgf/mm2 and maintains a high antifrictionality as a parameter that characterizes the dispersion interaction energy contribution to the total energy of the intermolecular interaction. The XPS examination of the copolymers has shown that only in the case of poly(arylene ether ketone) copolymer containing 10 mol % cardo groups, wear products do not undergo any considerable structural changes in the friction process. The studies demonstrated that a significant improvement of friction-and-wear parameters in the case of a poly(arylene ether ketone) copolymer containing a 10 mol % of cardo groups is caused by an optimal combination of increasing microhardness, formation of a discrete surface, and by maintaining a high antifrictionality. With increasing cardo group content in the copolymers to 15 and 25%, a gradual increase in the friction coefficient to 0.5 and 0.75, respectively, was observed.

Explicitly Correlated Dispersion and Exchange Dispersion Energies in Symmetry-Adapted Perturbation Theory.

The individual interaction energy terms in symmetry-adapted perturbation theory (SAPT) not only have different physical interpretations but also converge to their complete basis set (CBS) limit values at quite different rates. Dispersion energy is notoriously the slowest converging interaction energy contribution, and exchange dispersion energy, while smaller in absolute value, converges just as poorly in relative terms. To speed up the basis set convergence of the lowest-order SAPT dispersion and exchange dispersion energies, we borrow the techniques from explicitly correlated (F12) electronic structure theory and develop practical expressions for the closed-shell Edisp(20)-F12 and Eexch-disp(20)-F12 contributions. While the latter term has been derived and implemented for the first time, the former correction was recently proposed by Przybytek [ J. Chem. Theory Comput. 2018 , 14 , 5105 - 5117 ] using an Ansatz with a full optimization of the explicitly correlated amplitudes. In addition to reimplementing the fully optimized variant of Edisp(20)-F12, we propose three approximate Ansätze that substantially improve the scaling of the method and at the same time avoid the numerical instabilities of the unrestricted optimization. The performance of all four resulting flavors of Edisp(20)-F12 and Eexch-disp(20)-F12 is first tested on helium, neon, argon, water, and methane dimers, with orbital and auxiliary basis sets up to aug-cc-pV5Z and aug-cc-pV5Z-RI, respectively. The double- and triple-ζ basis set calculations are then extended to the entire A24 database of noncovalent interaction energies and compared with CBS estimates for Edisp(20) and Eexch-disp(20) computed using conventional SAPT with basis sets up to aug-cc-pV6Z with midbond functions. It is shown that the F12 treatment is highly successful in improving the basis set convergence of the SAPT terms, with the F12 calculations in an X-tuple ζ basis about as accurate as conventional calculations in bases with cardinal numbers (X + 2) for Edisp(20) and either (X + 1) or (X + 2) for Eexch-disp(20). While the full amplitude optimization affords the highest accuracy for both corrections, the much simpler and numerically stable optimized diagonal Ansatz is a very close second. We have also tested the performance of the simple F12 correction based on the second-order Møller-Plesset perturbation theory, SAPT-F12(MP2) [ Frey , J. A. ; Chem. Rev. 2016 , 116 , 5614 - 5641 ] and observed that it is also quite successful in speeding up the basis set convergence of conventional Edisp(20) + Eexch-disp(20), albeit with some outliers.

Interaction between islands in kinetic models of epitaxial growth of quantum dots

In the present paper, for the first time, the influence of interactions between 3D islands during epitaxial growth of quantum dots by Stranski–Krastanov mechanism is considered in the frames of kinetic models. The contribution of interaction energy between nanoclusters into the free energy of the system in the process of islands formation is estimated. In this approximation, critical thickness of transition from 2D to 3D growth, surface density and size distribution function of quantum dots are calculated with the help of the original model. The results of the work show that considering the interactions between islands is essential for precise evaluation of characteristics of the ensemble of quantum dots. Moreover, it is shown that neglecting this contribution leads to the prediction of higher surface densities and smaller sizes of quantum dots, which is the traditional problem of theoretical models. Accounting for the new factor gives unexpected result for the dependence of surface density of islands on deposition rate. These results are of paramount importance from the point of view of device applications of quantum dot heterostructures.

Nontrivial strength of van der Waals epitaxial interaction in soft perovskites

The van der Waals (vdW) bond is traditionally believed to be orders of magnitude lower than the typical chemical bond (i.e., ionic, metallic, or covalent), and hence the effects caused by a vdW interface are thought to be trivial. In this paper, by investigating the vdW epitaxial growth of a mechanically soft perovskite on the vdW substrate, we obtained the solid proof of strong non-negligible vdW interaction. The experimental results illustrate the formation of cracks and holes for the relaxation of the vdW strain as well as a lattice-constant-dependent epitaxial angle evolution and a pronounced band-structure change. The first-principles calculations indicate that the contribution of the vdW interaction energy at the epitaxial interface reaches up to more than a quarter of the overall interaction energy far exceeding the traditionally recognized vdW bonding strength. Both the experimental and the theoretical work show that given the appropriate material system, the vdW interaction could be strong enough to significantly manipulate material properties.

Correlation effects and many-body interactions in water clusters.

Background: The quantum-chemical description of the interactions in water clusters is an essential basis for deriving accurate and physically sound models of the interaction potential for water to be used in molecular simulations. In particular, the role of many-body interactions beyond the two-body interactions, which are often not explicitly taken into account by empirical force fields, can be accurately described by quantum chemistry methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field methods.Results: In line with earlier theoretical studies of the interactions in water clusters, it has been found that the main contribution to the many-body interactions in clusters with a size of up to N = 13 molecules are higher-order polarisation interaction terms. Compared to this, many-body dispersion interactions are practically negligible for all studied sytems. The two-body dispersion interaction, however, plays a significant role in the formation of the structures of the water clusters and their stability, since it leads to a distinct compression of the cluster sizes compared to the structures optimized on an uncorrelated level. Overall, the many-body interactions amount to about 13% of the total interaction energy, irrespective of the cluster size. The electron correlation contribution to these, however, amounts to only about 30% to the total many-body interactions for the largest clusters studied and is repulsive for all structures considered in this work.Conclusion: While this shows that three- and higher-body interactions can not be neglected in the description of water complexes, the electron correlation contributions to these are much smaller in comparison to the two-body electron correlation effects. Efficient quantum chemistry approaches for describing intermolecular interactions between water molecules may therefore describe higher-body interactions on an uncorrelated Hartree–Fock level without a serious loss in accuracy.

The Role of High Excitations in Constructing Sub-spectroscopic Accuracy Intermolecular Potential of He-HCN: Critically Examined by the High-Resolution Spectra with Resonance States

Interpreting high-resolution rovibrational spectra of weakly bound complexes commonly requires spectroscopic accuracy (&amp;lt;1 cm−1) potential energy surfaces (PES). Constructing high-accuracy ab initio PES relies on the high-level electronic structure approaches and the accurate physical models to represent the potentials. The coupled cluster approaches including single and double excitations with a perturbational estimate of triple excitations (CCSD(T)) have been termed the “gold standard” of electronic structure theory, and widely used in generating intermolecular interaction energies for most van der Waals complexes. However, for HCN-He complex, the observed millimeter-wave spectroscopy with high-excited resonance states has not been assigned and interpreted even on the ab initio PES computed at CCSD(T) level of theory with the complete basis set (CBS) limit. In this work, an effective three-dimensional ab initio PES for HCN-He, which explicitly incorporates dependence on the Q1 (C–H) normal-mode coordinate of the HCN monomer has been calculated at the CCSD(T)/CBS level. The post-CCSD(T) interaction energy has been examined and included in our PES. Analytic two-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies for v1(C–H)=0, and 1 to the Morse/Long-Range potential function form with root-mean-square deviations (RMSD) smaller than 0.011 cm−1. The role and significance of the post-CCSD(T) interaction energy contribution are clearly illustrated by comparison with the predicted rovibrational energy levels. With or without post-CCSD(T) corrections, the value of dissociation limit (D0) is 8.919 or 9.403 cm−1, respectively. The predicted millimeter-wave transitions and intensities from the PES with post-CCSD(T) excitation corrections are in good agreement with the available experimental data with RMS discrepancy of 0.072 cm−1. Moreover, the infrared spectrum for HCN-He complex is predicted for the first time. These results will serve as a good starting point and provide reliable guidance for future infrared studies of HCN doped in (He)n clusters.

Experimental and computational insights into energy contributions of intermolecular interactions

Experimental and computational insights into energy contributions of intermolecular interactions

Tuning of non-covalent interactions involving a halogen atom that plays the role of Lewis acid and base simultaneously

ABSTRACTIn this work, a series of model complexes (MH3X)(HNC)(N'C’H’), where M = C–Pb and X = Cl–At, is studied using a first-principles computational approach. Each of these complexes possesses a halogen atom (X) simultaneously acting as the Lewis base for X···H hydrogen bonding (HB) with HNC and as the Lewis acid for X···N’ halogen bonding (XB) with N'C’H’. The strengths of these non-covalent interactions are tuned by sharing the same halogen centre and by substituting M and X with consecutive elements from groups 14 and 17. Variations in the strengths are estimated mostly by means of various energetic quantities, such as the total interaction energy (Eint), two- and three-body contributions to Eint, their fundamental physical components and donor–acceptor orbital interaction energies. The coexistence of HB and XB involving the same X-centre weakens these interactions, but the magnitude of the total interaction in the complexes increases due to the three-body interaction and the appearance of additional lateral non-covalent interaction between HNC and N'C’H’. Substituting M and X with consecutive elements from groups 14 and 17 leads to several regularities in the changes of Eint. A dependence of three-body interaction on the kinds of M and X is also detected.