Change In Interaction Energy Research Articles

Quantum-mechanical evaluation of π-π versus substituent-π interactions in π stacking: direct evidence for the Wheeler-Houk picture.

The influence of substituents on π-stacking interactions has previously been explained by two competing hypotheses: a nonlocal effect in which tuning of the π density by the substituent alters the interaction (the Hunter-Sanders picture) or a local effect in which the direct interaction of the added substituent and changed polarity of the phenyl-substituent σ bond alter the interaction (the Wheeler-Houk picture). In this work, we applied the recently developed functional-group partition of symmetry-adapted perturbation theory (F-SAPT) to directly quantify these two effects in situ. The results show that both pictures contribute to the change in interaction energy but that the Wheeler-Houk picture is usually dominant.

Competition between halogen bond and hydrogen bond in complexes of superalkali Li3S and halogenated acetylene XCCH (X = F, Cl, Br, and I)

Complexes of superalkali Li3S and XCCH (X = F, Cl, Br, and I) have been studied with theoretical calculations at the MP2/aug‐cc‐pVTZ level. Three types of structures are found: (A) the X atom combines with the S atom through a halogen bond; (B) the X atom interacts with the π electron of Li3S by a π halogen bond; (C) the H atom combines with the S atom through a hydrogen bond. For A and B, a heavier halogen atom makes the interaction stronger, while for C, the change of interaction energy is not obvious, showing a small dependence on the nature of the X atom in HCCX. A is more stable than B and their difference in stability decreases as X varies from Cl to I. For the F and Cl complexes, A is weaker than C, however, the former is stronger than the latter in the Br and I complexes. The above three types of interactions have been analyzed by means of electron localization function, electron density difference, and energy decomposition, and the results show that they have similar nature and features with conventional interactions. © 2014 Wiley Periodicals, Inc.

A report of rifampin-resistant leprosy from northern and eastern India: identification and in silico analysis of molecular interactions

Presence of point mutations within the drug resistance determining regions of Mycobacterium leprae (M. leprae) genome confers molecular basis of drug resistance to dapsone, rifampin and ofloxacin in leprosy. This study is focused on the identification of mutations within the rpoB gene region of M. leprae that are specific for rifampin interaction, and further in silico analysis was carried out to determine the variations in the interactions. DNA and RNA were isolated from slit skin scrapings of 60 relapsed leprosy patients. PCR targeting rpoB gene region and amplicon sequencing was performed to determine point mutations. mRNA expression levels of rpoB and high-resolution melt analysis of mutants were performed using Rotor Gene Q Realtime PCR. Molecular docking was performed using LigandFit Software. Ten cases having point mutations within the rpoB gene region were identified and were clinically confirmed to be resistant to rifampin. A new mutation at codon position Gln442His has been identified. There is a 9.44-fold upregulation in the mRNA expression of rpoB gene in mutant/resistant samples when compared with the wild/sensitive samples. In silico docking analysis of rifampin with wild-type and Gln442His mutant RpoB proteins revealed a variation in the hydrogen-bonding pattern leading to a difference in the total interaction energy and conformational change at position Asp441. These preliminary downstream functional observations revealed that the presence of point mutations within the rifampin resistance determining regions of rpoB gene plays a vital role in conferring genetic and molecular basis of resistance to rifampin in leprosy.

A B3LYP and MP2(full) theoretical investigation into cooperativity effects, aromaticity and thermodynamic properties in the Na+⋯benzonitrile⋯H2O ternary complex

The cooperativity effects between H-bonding and Na(+)⋯π or Na(+)⋯σ interactions in Na(+)⋯benzonitrile⋯H2O complexes were investigated using the B3LYP and MP2(full) methods with 6-311++G(2d,p) and aug-cc-pVTZ basis sets. The thermodynamic cooperativity and the influence of this cooperativity on aromaticity was evaluated by nucleus-independent chemical shifts (NICS). The results showed that the influence of the Na(+)⋯σ or Na(+)⋯π interaction on the hydrogen bond is more pronounced than that of the latter on the former. The cooperativity effect appeared in the Na(+)⋯σ interaction complex while the anti-cooperativity effect tended to be in the Na(+)⋯π system. The change in enthalpy is the major factor driving cooperativity. Thermodynamic cooperativity is not in accordance with the cooperativity effect evaluated by the change of interaction energy. The ring aromaticity of is weakened while the bond dissociation energy (BDE) of the C-CN bond increases upon ternary complex formation. The cooperativity effect (E coop) correlates with R c (NICS(1)ternary/NICS(1)binary) and ΔΔδ (Δδ ternary - Δδ binary) involving the ring and C ≡ N bond, as well as R BDE(C-CN) [BDE(C-CN)ternary/BDE(C-CN)binary], respectively. AIM (atoms in molecules) analysis confirms the existence of cooperativity.

Hydrogen-bonded complexes upon spatial confinement: structural and energetic aspects

In the present study we consider structural and energetic aspects of spatial confinement of the H-bonded systems. The model dimeric systems: HF···HF, HCN···HCN and HCN···HCCH have been chosen for a case study. Two-dimensional harmonic oscillator potential, mimicking a cylindrical confinement, was applied in order to render the impact of orbital compression on the analyzed molecular complexes. The calculations have been performed employing the MP2 method as well as the Kohn-Sham formulation of density functional theory. In the latter case, two exchange-correlation potentials have been used, namely B3LYP and M06-2X. The geometries of studied complexes have been optimized (without any constraints) in the presence of the applied model confining potential. A thorough analysis of topological parameters characterizing hydrogen bonds upon orbital compression has been performed within the Quantum Theory of Atoms in Molecules (QTAIM). Furthermore, an energetic analysis performed for the confined H-bonded complexes has shown a different trend in the interaction energy changes. Additionally, a variational-perturbational decomposition scheme was applied to study the interaction energy components in the presence of spatial confinement.

Ion effects at electrode/solid polymer electrolyte membrane interfaces

The differential capacity and the potential distribution at electrode/solid polymer electrolyte membrane/solution interfaces are calculated through an analytical approach. The model considers coions' and counterions' permeation through the membrane from the solvent phase and the ions' partitioning equilibrium at the SPEM/solution interface. The latter effects are included by incorporating the Donnan equilibrium, the steric hindrance, the solvation energy change when ions move from water to membrane pores and ion electrostatic interactions. It is shown that capacitance maxima in capacitance-potential curves may appear because of the acid-base dissociation process inside the membrane and the change in the ions' total interaction energy with the applied potential. For low dielectric constants inside membrane pores, εp, sharp peaks can be obtained. These peaks broaden, decrease in magnitude and shift to positive potentials once εp is increased. Finally, model predictions are discussed in light of recent experimental data obtained on Nafion® covered Pt(111) electrodes, providing a theoretical framework for the qualitative electroanalysis of these systems.

Comparison of substitution effects of F and methyl groups adjoined to C and B atoms in hydrogen bonds

Ab initio calculations have been performed for the complexes of pyridine with 1,2-dihydro-1,2-azaborine (1), 1,3-dihydro-1,3-azaborine (2), 1,4-dihydro-1,4-azaborine (3), and their F and methyl derivatives to compare the influence of both substituents adjoined to the C and B atoms on the strength of hydrogen bonding. The NH⋯N hydrogen bond is enhanced by the substituent F whether it is connected to C or B atom, and the enhancing effect is bigger for one bonded to the C atom. The role of methyl group depends on the position of the substitution. NBO analyses showed that H, F, and methyl substituents are electron-withdrawing in the formation of complexes, but the electron-withdrawing ability of the methyl group bonded to the B atom is smaller than that of the corresponding H atom. The cooperativity between different types of interactions in 1 and its derivatives has also been discussed in the change of interaction energy and binding distance.

Spin-orbit interaction in a quantum pseudodot: pressure effect

In the present work, the Schrodinger equation for a pseudo-dot is solved analytically by using the Laplace transformation. Then, by using the variational procedure, the donor binding energy is calculated with a hydrogenic donor impurity at the center. Finally, the hydrostatic pressure effect on the spin-orbit interaction and the binding energy is studied. According to the obtained results, it is found that the binding energy increases with increasing pressure. The level splitting due to the spin-orbit interaction increases by increasing pressure. The splitting decreases with increasing pseudodot size. The change of spin-orbit interaction energy for a GaAs quantum pseudo-dot is very small due to the pressure even at very low temperature.

Phenotypic detection and structure analysis of a PC missense mutation (Met406Ile) resulted in venous thromboembolism

To identify the phenotypic detection and structure analysis of a protein C (PC) missense mutation (Met406Ile) resulting in venous thromboembolism. Pedigree research was performed for a hereditary PC deficiency pedigree. Chromogenic assay was used for phenotypic diagnosis to detect the AT activity. All 9 exons were amplified by polymerase chain reaction (PCR) and direct sequencing analysis was performed for PCR products. The corresponding mutation sites of family members were detected.Homology modeling was used for reconstructing mutant PC construction. The effects of construction change were analyzed. The PC activities of proband and 4 family members decreased to different extents by 29.7%, 42.2%, 42.4%, 67.3% and 70.7% respectively. Among them, the proband and other three family members carried the same mutation (c.1218G > A, Met406Ile) while another family member had a PC polymorphism (rs1799810). Homology modeling showed that VDW's interaction radius of amino acids decreased after mutation (Met406Ile).In particular, the radius of Gly418:C and Ile406CG2, Gly418:C and Ile406HG23, Leu419:N and Ile406:HG23 decreased to 2.0733å, 1.620 45å and 1.446 52å respectively. Compared with normal PC, the interaction energy of mutant PC rose from -8.504 54 to 1210.04 kal/mol. And the change of VDW interaction energy was significant. The mechanism of this pedigree is caused by PROC gene missense mutation on exon 9 (c.1218G > A, Met406Ile). The regional amino acids of mutant PC collide with each other and lead to an instability of PC reconstruction.

Recognition of protein folding kinetics pathways based on amino acid properties information derived from primary sequence

Recognition of protein folding kinetics pathways is an effective approach for the study of protein folding behaviors, and thereby to get a better understanding of mechanism that how a protein folds into a functional structure. In this study, we presented a novel method for the classification of protein folding kinetics pathways based on a new class of features weighted by amino acid properties, which were derived from protein primary sequence. According to the leave-one-out and bootstrap cross-validation results, the model with eight features was the best one, and it achieved a satisfactory prediction accuracy of 91.67% for training set; while n-fold cross-validation had also been performed and the results showed that the built model was stable. Besides, the external test set was employed to evaluate the predictive ability of the built model. The accuracy for external test set achieved 88.24% and MCC was 0.79. Next, the selected important features were analyzed for a better understanding of the protein folding mechanisms. The analysis suggests that long-range interaction and unfolding Gibbs free energy change are important factors in determining the protein folding kinetics pathways. Besides, hydrophobicity, secondary structure and charges are also implied to be the important properties that affect the behavior of protein folding.

Aluminium distribution in ZSM-5 revisited: The role of Al–Al interactions

We present a theoretical study of the distribution of Al atoms in zeolite ZSM-5 with Si/Al=47, where we focus on the role of Al–Al interactions rather than on the energetics of Al/Si substitutions at individual sites. Using interatomic potential methods, we evaluate the energies of the full set of symmetrically independent configurations of Al siting in a Si94Al2O192 cell. The equilibrium Al distribution is determined by the interplay of two factors: the energetics of the Al/Si substitution at an individual site, which tends to populate particular T sites (e.g., the T14 site), and the Al–Al interaction, which at this Si/Al maximises Al–Al distances in general agreement with Dempsey’s rule. However, it is found that the interaction energy changes approximately as the inverse of the square of the distance between the two Al atoms, rather than the inverse of the distance expected if this were merely charge repulsion. Moreover, we find that the anisotropic nature of the framework density plays an important role in determining the magnitude of the interactions, which are not simply dependent on Al–Al distances.

Computational study on interaction energy changes during double proton transfer process

This paper reports the computational studies on the double proton transfer for: the formamide–formic acid, FM⋯FA and formamide–formamidine, FM⋯FI. Despite being accurate, total interaction energy does not provide any information about its partitioning into physically defined energy terms. The Symmetry-Adapted Perturbation Theory interaction-energy decomposition along the intrinsic reaction coordinates connecting the two equilibrium geometries via the transition state has been analyzed. No one term of the interaction energy was found to be solely responsible for the changes of interaction energy along the whole DPT path; however, the exchange and the induction terms have a major contribution.

Ring Substituents on Substituted Benzamide Ligands Indirectly Mediate Interactions with Position 7.39 of Transmembrane Helix 7 of the D4 Dopamine Receptor

In an effort to delineate how specific molecular interactions of dopamine receptor ligand classes vary between D2-like dopamine receptor subtypes, a conserved threonine in transmembrane (TM) helix 7 (Thr7.39), implicated as a key ligand interaction site with biogenic amine G protein-coupled receptors, was substituted with alanine in D2 and D4 receptors. Interrogation of different ligand chemotypes for sensitivity to this substitution revealed enhanced affinity in the D4, but not the D2 receptor, specifically for substituted benzamides (SBAs) having polar 4- (para) and/or 5- (meta) benzamide ring substituents. D4-T7.39A was fully functional, and the mutation did not alter the sodium-mediated positive and negative allostery observed with SBAs and agonists, respectively. With the exception of the non-SBA ligand (+)-butaclamol, which, in contrast to certain SBAs, had decreased affinity for the D4-T7.39A mutant, the interactions of numerous other ligands were unaffected by this mutation. SBAs were docked into D4 models in the same mode as observed for eticlopride in the D3 crystal structure. In this mode, interactions with TM5 and TM6 residues constrain the SBA ring position that produces distal steric crowding between pyrrolidinyl/diethylamine moieties and D4-Thr7.39. Ligand-residue interaction energy profiles suggest this crowding is mitigated by substitution with a smaller alanine. The profiles indicate sites that contribute to the SBA binding interaction and site-specific energy changes imparted by the D4-T7.39A mutation. Substantial interaction energy changes are observed at only a few positions, some of which are not conserved among the dopamine receptor subtypes and thus seem to account for this D4 subtype-specific structure-activity relationship.

Intrinsic electronic reorganization energy in the electron transfer from substituted N,N-dimethylanilines to phthalimide N-oxyl radical

The usefulness of global descriptors based on the density functional theory framework has been discussed in the context of electron transfer reactions. A simple relationship between the vertical electronic energy associated to the complete ET transfer process and the change of interaction energy associated to the D–A couple of reagents (i.e., the assorted electronic hardness), provides an immediate connection to the intrinsic electronic reorganization energy of the reaction process. Theoretical results for the recently proposed electron transfer process from substituted N,N-dimethylanilines to phthalimide N-oxyl radical, are in complete agreement with the kinetic and substituent effects experimentally available evidence.

Transition Metal Hydrazide‐Based Hydrogen‐Storage Materials: the First Atoms‐In‐Molecules Analysis of the Kubas Interaction

Molecular models of the M-H(2) binding sites of experimentally characterised amorphous vanadium hydrazide gels are studied computationally using gradient corrected density functional theory, to probe the coordination number of the vanadium in the material and the nature of the interaction between the metal and the H(2) molecules. The H(2) is found to bind to the vanadium through the Kubas interaction, and the first quantum theory of atoms-in-molecules analysis of this type of interaction is reported. Strong correlation is observed between the electron density at the H-H bond critical point and the M-H(2) interaction energy. Four coordinate models give the best reproduction of the experimental data, suggesting that the experimental sites are four coordinate. The V-H(2) interaction is shown to be greater when the non-hydrazine based ligand, THF, of the experimental system is altered to a poorer π-acceptor ligand. Upon altering the metal to Ti or Cr the M-H(2) interaction energy changes little but the number of H(2) which may be bound decreases from four (Ti) to two (Cr). It is proposed that changing the metal from V to Ti may increase the hydrogen storage capacity of the experimental system. A 9.9 wt% maximum storage capacity at the ideal binding enthalpy for room temperature performance is predicted when the Ti metal is combined with a coordination sphere containing 2 hydride ligands.

Understanding the desensitizing mechanism of olefin in explosives: shear slide of mixed HMX-olefin systems

We simulated the shear slide behavior of typical mixed HMX-olefin systems and the effect of thickness of olefin layers (4-22 Å) on the behavior at a molecular level by considering two cases: bulk shear and interfacial shear. The results show that: (1) the addition of olefin into HMX can reduce greatly the shear sliding barriers relative to the pure HMX in the two cases, suggesting that the desensitizing mechanism of olefin is controlled dominantly by its good lubricating property; (2) the change of interaction energy in both systoles of shear slide is strongly dominated by van der Waals interaction; and (3) the thickness of olefin layers in the mixed explosives can influence its desensitizing efficiency. That is, the excessive thinness of olefin layers in the mixed explosive systems, for example, several angstroms, can lead to very high sliding barriers.

Phase equilibrium of PuO 2− x − Pu 2O 3 based on first-principles calculations and configurational entropy change

Combination of an oxygen vacancy formation energy calculated using first-principles approach and the configurational entropy change treated within the framework of statistical mechanics gives an expression of the Gibbs free energy at large deviation from stoichiometry of plutonium oxide PuO 2. An oxygen vacancy formation energy 4.20 eV derived from our previously first-principles calculation was used to evaluate the Gibbs free energy change due to oxygen vacancies in the crystal. The oxygen partial pressures then can be evaluated from the change of the free energy with two fitting parameters (a vacancy–vacancy interaction energy and vibration entropy change due to induced vacancies). Derived thermodynamic expression for the free energy based on the SGTE thermodynamic data for the stoichiometric PuO 2 and the Pu 2O 3 compounds was further incorporated into the CALPHAD modeling, then phase equilibrium between the stoichiometric Pu 2O 3 and non-stoichiometric PuO 2− x were reproduced.

Plasmonic contribution to the van der Waals energy in strongly interacting bilayers

We investigate the van der Waals or interaction energy due to the plasmon modes in bilayer fermion and boson systems for several layer separation and coupling strength values. Interaction effects are studied within the random-phase approximation (RPA), the quasilocalized charge approximation (QLCA), and the Singwi, Tosi, Land, and Sj\olander (STLS) models of the dielectric function formalism. We find that the interaction becomes repulsive at short separation distances for strongly coupled systems described by the QLCA and STLS approaches in contrast to attractive behavior predicted by the RPA. At larger separation distances, the interaction energy changes sign within the QLCA and STLS models leading to an attractive interaction. The evident relation between our calculations and the Casimir effect is emphasized.

Ab initio MO Study of Hydrogen Bonding and Spectral Characteristics of HCN-H2O-HCN Trimer: Comparison between Dimer and Trimer

Hydrogen bonding of HCN-H2O-HCN trimer has been studied by means of ab initio molecular orbital (MO) calculations. The changes in intermolecular interaction energy and vibrational frequency induced by addition of HCN molecule to HCN-H2O or H2O-HCN dimer are especially focused. The distances of hydrogen bonds in the trimer are calculated to be shorter than those in the corresponding dimers. The hydrogen bond distances are hence shortened by addition of another HCN. The interaction energies of the hydrogen bonds are also increased by addition of HCN. The dipole moment of the trimer is smaller than the sum of the dipole moments of the separate moieties (HCN + H2O + HCN). This is opposite of the previous result for H2O-HCN-H2O. The spectral shift of the stretching modes induced by hydrogen bond formation has been predicted by vibrational frequency analysis. The vibrational frequency of the asymmetric stretching mode of HCN included in the H2O-HCN part of the trimer is remarkably red-shifted from that of the H2O-HCN dimer. This information is expected to be useful for experimental detection of the trimer.

Relationship Between Conformational Changes in Pol λ’s Active Site Upon Binding Incorrect Nucleotides and Mismatch Incorporation Rates

The correct replication and repair of DNA is critical for a cell's survival. Here, we investigate the fidelity of mammalian DNA polymerase lambda (pol lambda) utilizing dynamics simulation of the enzyme bound to incorrect incoming nucleotides including A:C, A:G, A(syn):G, A:A, A(syn):A, and T:G, all of which exhibit differing incorporation rates for pol lambda as compared to A:T bound to pol lambda. The wide range of DNA motion and protein residue side-chain motions observed in the mismatched systems demonstrates distinct differences when compared to the reference (correct base pair) system. Notably, Arg517's interactions with the DNA template strand bases in the active site are more limited, and Arg517 displays increased interactions with the incorrect dNTPs. This effect suggests that Arg517 helps provide a base-checking mechanism to discriminate correct from incorrect dNTPs. In addition, we find Tyr505 and Phe506 also play key roles in this base checking. A survey of the electrostatic potential landscape of the active sites and concomitant changes in electrostatic interaction energy between Arg517 and the dNTPs reveals that pol lambda binds incorrect dNTPs less tightly than the correct dNTP. These trends lead us to propose the following order for mismatch insertion by pol lambda: A:C > A:G > A(syn):G > T:G > A(syn):A > A:A. This sequence agrees with available kinetic data for incorrect nucleotide insertion opposite template adenine, with the exception of T:G, which may be more sensitive to the insertion context.