Energy Decomposition Method Research Articles

Electronic Structure and Bonding Situation in M2O2 (M = Be, Mg, Ca) Rhombic Clusters.

Quantum chemical calculations using ab initio methods at the CCSD(T) level and density functional theory have been carried out for the title molecules. The electronic structures of the molecules were analyzed with a variety of charge and energy decomposition methods. The equilibrium geometries of the M2O2 rhombic clusters exhibit very short distances between the transannular metal atoms M = Be, Mg, Ca. The calculated distances are close to standard values between double and triple bonds, but there are no chemical M-M bonds. The metal atoms M carry large positive partial charges, which are even bigger than in diatomic MO. The valence electrons of M are essentially shifted toward oxygen in M2O2, which makes it possible that there is practically no electronic charge in the region between the metal atoms. The bond dissociation energies for fragmentation of M2O2 into two metal oxides MO are very large. The metal-oxide bonds in the rhombic clusters are shorter and stronger than in diatomic MO. A detailed analysis of the electronic structure suggests that there is no significant direct M-M interaction in the M2O2 rhombic clusters, albeit weak three-center M-O-M bonding.

Effect of double mutations T790M/L858R on conformation and drug-resistant mechanism of epidermal growth factor receptor explored by molecular dynamics simulations.

Epidermal growth factor receptor (EGFR) is one of the most promising targets for the treatment of cancers. Double mutations T790M/L858R lead to different degrees of drug resistance toward inhibitors. In this study, molecular dynamics (MD) simulations followed by principal component analysis are performed to study the conformational changes of EGFR induced by T790M/L858R. The results suggest that T790M/L858R cause obvious disturbance of the structural stability of EGFR. Molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) and residue-based free energy decomposition methods are integrated to explore the drug-resistant mechanism of T790M/L858R toward inhibitors. The results show that the decrease in van der Waals interactions of inhibitors with the mutated EFGR relative to the wild-type (WT) one is the main force inducing drug resistance of T790M/L858R toward inhibitors TAK-285, while drug resistance toward W2P and HKI-272 is dominated by the decrease in van der Waals interactions and the increase in polar interactions. We expect that the information obtained from this study can aid rational design of effective drugs to relieve drug resistance of EGFR induced by T790M/L858R.

Comparative diagnostic accuracy of dual-energy CT myocardial perfusion imaging by monochromatic energy versus material decomposition methods

PurposeTo compare the diagnostic value of monochromatic and material decomposition (MD) dual- energy computed tomography (DECT) imaging for the evaluation of ischemia. MethodsPatients with suspected coronary artery disease underwent rest-stress DECT and SPECT perfusion imaging. DECT images were reconstructed between 40 and 140keV and through MD of iodine/muscle. ResultsMD and monochromatic imaging had a sensitivity, specificity, negative predictive, positive predictive value, and accuracy of 89%, 40%, 67%, 73% and 71%; and 91%, 67%, 67%, 91% and 86%, respectively (p=0.05). ConclusionDECT using monochromatic energy displayed a non-significantly higher diagnostic accuracy for myocardial ischemia as compared with DECT MD.

Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations

Endocellular protein tyrosine phosphatase 1B (PTP1B) is one of the most promising target for designing and developing drugs to cure type-II diabetes and obesity. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) and solvated interaction energy methods were applied to study binding differences of three inhibitors (ID: 901, 941, and 968) to PTP1B, the calculated results show that the inhibitor 901 has the strongest binding ability to PTP1B among the current inhibitors. Principal component (PC) analysis was also carried out to investigate the conformational change of PTP1B, and the results indicate that the associations of inhibitors with PTP1B generate a significant effect on the motion of the WPD-loop. Free energy decomposition method was applied to study the contributions of individual residues to inhibitor bindings, it is found that three inhibitors can generate hydrogen bonding interactions and hydrophobic interactions with different residues of PTP1B, which provide important forces for associations of inhibitors with PTP1B. This research is expected to give a meaningfully theoretical guidance to design and develop of effective drugs curing type-II diabetes and obesity.

Flow noise identification using acoustic emission (AE) energy decomposition for sand monitoring in flow pipeline

In pipelines used for petroleum production and transportation, sand particles may be present in the multi-phase flow of oil and gas and water. The Acoustic Emission (AE) measurement technique is used in the field of sand monitoring and detection in the oil and gas industry. However, as the AE signals recorded are strongly influenced by flow conditions in the pipe, identification of sand particle related signals or events remain a significant challenge in interpretation of AE signals. Therefore, a systematic investigation of sand particle impact AE energy measurements, using a sensor mounted on the outer surface of a sharp bend in a carbon steel pipe, was carried out in the laboratory to characterise flow signals using a slurry impingement flow loop test rig. A range of silica sand particles fractions of mean particle size (212–710 μm) were used in the flow with particle nominal concentration between (1 and 5 wt.%) while the free stream velocity was changed between (4.2 and 14 ms−1).A signal processing technique was developed in which the total AE energy associated with particle-free water impingement was divided into static and oscillated parts and a demodulated frequency analysis was carried out on the oscillated part to identify major spectral components and hence the sources of AE signals. A simple theoretical model for water impingement AE signals was then developed to show the dependence of AE energy components on different flow speeds. A similar decomposition of AE energy into static and oscillatory components was used to analyse AE signals for particle-laden flows. The effect of flow speed on the spectral AE energy for different sand concentrations and particle size fractions was investigated and the results show that the 100 Hz band is attributed to mechanical noise, the 42 Hz band is due to fluid turbulence and the dominant band is broad oscillated component.The AE energy decomposition method together with the water impingement model and coupled with spectral peaks filtering enable isolation of AE energy associated with particle impact from other AE sources and noise and, hence, the proposed decomposition approach can enhance the interpretation of AE data in pipeline flows.

Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field.

The interactions between metal ions and proteins are ubiquitous in biology. The selective binding of metal ions has a variety of regulatory functions. Therefore, there is a need to understand the mechanism of protein-ion binding. The interactions involving metal ions are complicated in nature, where short-range charge-penetration, charge transfer, polarization, and many-body effects all contribute significantly, and a quantitative description of all these interactions is lacking. In addition, it is unclear how well current polarizable force fields can capture these energy terms and whether these polarization models are good enough to describe the many-body effects. In this work, two energy decomposition methods, absolutely localized molecular orbitals and symmetry-adapted perturbation theory, were utilized to study the interactions between Mg2+/Ca2+ and model compounds for amino acids. Comparison of individual interaction components revealed that while there are significant charge-penetration and charge-transfer effects in Ca complexes, these effects can be captured by the van der Waals (vdW) term in the AMOEBA force field. The electrostatic interaction in Mg complexes is well described by AMOEBA since the charge penetration is small, but the distance-dependent polarization energy is problematic. Many-body effects were shown to be important for protein-ion binding. In the absence of many-body effects, highly charged binding pockets will be over-stabilized, and the pockets will always favor Mg and thus lose selectivity. Therefore, many-body effects must be incorporated in the force field in order to predict the structure and energetics of metalloproteins. Also, the many-body effects of charge transfer in Ca complexes were found to be non-negligible. The absorption of charge-transfer energy into the additive vdW term was a main source of error for the AMOEBA many-body interaction energies.

Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations.

In this work, we evaluate the accuracy of the classical AMOEBA model for representing many-body interactions, such as polarization, charge transfer, and Pauli repulsion and dispersion, through comparison against an energy decomposition method based on absolutely localized molecular orbitals (ALMO-EDA) for the water trimer and a variety of ion-water systems. When the 2- and 3-body contributions according to the many-body expansion are analyzed for the ion-water trimer systems examined here, the 3-body contributions to Pauli repulsion and dispersion are found to be negligible under ALMO-EDA, thereby supporting the validity of the pairwise-additive approximation in AMOEBA's 14-7 van der Waals term. However AMOEBA shows imperfect cancellation of errors for the missing effects of charge transfer and incorrectness in the distance dependence for polarization when compared with the corresponding ALMO-EDA terms. We trace the larger 2-body followed by 3-body polarization errors to the Thole damping scheme used in AMOEBA, and although the width parameter in Thole damping can be changed to improve agreement with the ALMO-EDA polarization for points about equilibrium, the correct profile of polarization as a function of intermolecular distance cannot be reproduced. The results suggest that there is a need for re-examining the damping and polarization model used in the AMOEBA force field and provide further insights into the formulations of polarizable force fields in general.

Estimating and modeling charge transfer from the SAPT induction energy.

Recent studies using quantum mechanics energy decomposition methods, for example, SAPT and ALMO, have revealed that the charge transfer energy may play an important role in short ranged inter-molecular interactions, and have a different distance dependence comparing with the polarization energy. However, the charge transfer energy component has been ignored in most current polarizable or non-polarizable force fields. In this work, first, we proposed an empirical decomposition of SAPT induction energy into charge transfer and polarization energy that mimics the regularized SAPT method (ED-SAPT). This empirical decomposition is free of the divergence issue, hence providing a good reference for force field development. Then, we further extended this concept in the context of AMOEBA polarizable force field, proposed a consistent approach to treat the charge transfer phenomenon. Current results show a promising application of this charge transfer model in future force field development. © 2017 Wiley Periodicals, Inc.

Structures, Energies, and Bonding Analysis of Monoaurated Complexes with N-Heterocyclic Carbene and Analogues

In this work, we computationally investigated from quantum chemical calculations (DFT) at the BP86 level with the various basis sets def2-SVP, def2-TZVPP, and TZ2P+, chemical bonding issues of the recently described carbene-analogues gold(I) complexes AuCl-NHEMe (Au1-NHE) with E = C – Pb. The optimized structures and the metal-ligand bond dissociation energy (BDE) were calculated, and the nature of the E→Au bond was studied with charge and energy decomposition methods. The equilibrium structures of the system showed that there were major differences in the bonded orientation from the ligands NHC-NHPb to gold(I) complex between the lighter and the heavier homologues. The BDEs results showed that the metal-carbene analogues bonds were very strong bonds and the strongest bond was calculated for Au1-NHC which had the bond strength De = 79.2 kcal/mol. Bonding analysis of Au1-NHE showed that NHE ligands exhibited donor-acceptor bonds with the σ lone pair electrons of NHE donated into the vacant orbital of the acceptor fragment (AuCl). The EDA-NOCV results indicated that the ligand NHE in Au1-NHE complexes were strong σ-donors and very weak π donor and the bond order in complexes was Au1-NHC > Au1-NHSi > Au1-NHGe > Au1-NHSn > Au1-NHPb. We also realised that the gold-ligand bond was characterized by a π back-donation component from the Au to the ligand. All investigated complexes in this study were suitable targets for synthesis and gave a challenge in designing Au nano-crystals of narrow size distribution from gold(I) complexes that carried versatile N-heterocyclic carbene-analogues NHE.

Can Tetrylone Act in a Similar Fashion to Tetrylene in Ni(CO)2 Complexes? A Theoretical Study based on a Comparison using DFT Calculations

A comparison was made to investigate the structures and bonding of nickel complex that carry tetrylone and tetrylene ligands [(CO)2Ni‐{E(PH3)2}] (Ni1E) and [(CO)2Ni‐{NHEMe}] (Ni2E) (E = C to Pb) using quantum chemical calculations at the BP86 level with various basis sets (SVP, TZVPP, TZ2P+). The nature of the Ni–E bonds was analyzed with charge‐ and energy decomposition methods. The structures of tetrylone complexes Ni1E exhibit an interesting trend with the ligands E(PH3)2 are bonded in a tilted orientation relative to the fragment Ni(CO)2. In contrast, the calculated equilibrium structures of complexes Ni2E exhibit the NHEMe ligands (E = C to Sn) bonded in a head‐on way to the Ni(CO)2 fragment, while the bending angle gives the strongest side‐on bonded ligand NHPbMe when E = Pb. The interesting trend of the bond dissociation energy (BDE) is observed for the tetrylone, which has the same trend BDEs compared with tetrylene complexes. The EDA‐NOCV results indicate that the tetrylone ligands {E(PH3)2} in complexes are similar to the tetrylene ligands NHEMe as strong σ‐donors and weak π‐acceptors. The BDEs calculated for the Ni–E bonds in Ni1E and Ni2E show that the effect of bulky ligands may obscure the intrinsic Ni–E bond strength. The bonding analysis shows that the tetrylone ligands in Ni1E may act in a similar fashion to the tetrylene ligands in Ni2E. All complexes Ni1E and Ni2E are suitable targets for synthesis.

Hydrogen bonded dimers of small alkyl substituted amides: Structures, energetics, and spectral analyses based on density functional theory calculations

We have performed a density functional theory (DFT) study on the hydrogen bonding patterns for the dimers of small alkyl substituted amides, including formamide, acetamide, and propionamide, as well as their N-methyl substituted counterparts. The dispersion-corrected ωB97X-D exchange-correlation density functional with the aug-cc-pVDZ basis set has been employed in the energy and frequency calculations. To calibrate the DFT calculated binding energies for these dimeric complexes, we perform a benchmark calculation with the coupled cluster with single, double and perturbative triple excitations method at the complete basis set limit [CCSD(T)/CBS]. The binding energies are further analyzed by the energy decomposition method based on the symmetry adapted perturbation theory. The infrared spectra for the alkyl substituted amides and their dimers are simulated with explicit anharmonicities included, and compared with the representative experimental data. Both the dimer formations and the anharmonic corrections have significant effects on the principal spectral features related to hydrogen bonding, while the substitution effects are comparatively marginal.

Insight into binding mechanisms of inhibitors MKP56, MKP73, MKP86, and MKP97 to HIV-1 protease by using molecular dynamics simulation

HIV-1 protease (PR) has been a significant target for design of potent inhibitors curing acquired immunodeficiency syndrome. Molecular dynamics simulations coupled with molecular mechanics Poisson–Boltzmann surface area method were performed to study interaction modes of four inhibitors MKP56, MKP73, MKP86, and MKP97 with PR. The results suggest that the main force controlling interactions of inhibitors with PR should be contributed by van der Waals interactions between inhibitors and PR. The cross-correlation analyses based on MD trajectories show that inhibitor binding produces significant effect on the flap dynamics of PR. Hydrogen bond analyses indicate that inhibitors can form stable hydrogen bonding interactions with the residues from the catalytic strands of PR. The contributions of separate residues to inhibitor bindings are evaluated by using residue-based free energy decomposition method and the results demonstrate that the CH–π and CH–CH interactions between the hydrophobic groups of inhibitors with residues drive the associations of inhibitors with PR. We expect that this study can provide a significant theoretical aid for design of potent inhibitors targeting PR.

Carbones as Ligands in Novel Main-Group Compounds E[C(NHC)2 ]2 (E=Be, B+ , C2+ , N3+ , Mg, Al+ , Si2+ , P3+ ): A Theoretical Study.

Quantum chemical calculations of the main-group compounds E[C(NHCMe )2 ]2 (E=Be, B+ , C2+ , N3+ , Mg, Al+ , Si2+ , P3+ ) have been carried out using density functional theory at the BP86/def2-TZVPP and BP86-D3(BJ)/def2-TZVPP levels of theory. The geometry optimization at BP86/def2-TZVPP gives equilibrium structures with two-coordinated species E and bending angles C-E-C between 152.5° (E=Be) and 110.5° (E=Al). Inclusion of dispersion forces at BP86-D3(BJ)/def2-TZVPP yields a three-coordinated beryllium compound Be[C(NHCMe )2 ]2 as the only energy minimum form. Three-coordinated isomers are found besides the two-coordinated energy minima for the boron and carbon cations B[C(NHCMe )2 ]2+ and C[C(NHCMe )2 ]22+ . The three-coordinated form of the boron compound is energetically lower lying than the two-coordinated form, while the opposite trend is calculated for the carbon species. The theoretically predicted bond dissociation energies suggest that all compounds are viable species for experimental studies. The X-ray structure of the benzoannelated homologue of P[C(NHCMe )2 ]23+ that was recently reported by Dordevic et al. agrees quite well with the calculated geometry of the molecule. A detailed bonding analysis using charge and energy decomposition methods shows that the two-coordinated neutral compounds Be[C(NHCMe )2 ]2 and Mg[C(NHCMe )2 ]2 possess strongly positively charged atoms Be and Mg. The carbodicarbene groups C(NHCMe )2 serve as acceptor ligands in the compounds and may be sketched with dative bonds (NHCMe )2 C←E→C(NHCMe )2 (E=Be, Mg). Dative bonds in which the carbones C(NHCMe )2 are donor ligands are suggested for the cations (NHCMe )2 C→E←C(NHCMe )2 (E=B+ , Al+ ). The dications and trications possess electron-sharing bonds in which the bonding situation is best described with the formula [(NHCMe )2 C]+ -E-[C(NHCMe )2 ]+ (E=C, Si, N+ , P+ ).

Bonding Situation of Bis-gold Chloride Complexes with N-heterocyclic Carbene-Analogues [(AuCl)2-NHEMe] (E=C – Pb) based on DFT Calculations

Abstract We computationally investigated the structure and bonding situation of bis-gold chloride complexes, (AuCl)2, containing N-heterocyclic carbenes and analogues, called tetrylenes [(AuCl)2-NHEMe] (Au2-NHE) with E=C to Pb, using density functional theory (DFT) at the BP86 level with the basis sets def2-SVP, def2-TZVPP, and TZ2P+. The nature of the (AuCl)2-NHEMe bond in the Au2-NHE complexes was analyzed using charge and energy decomposition methods. The calculated equilibrium structures of the Au2-NHE complexes showed that the tetrylene ligands, NHEMe (E=C to Ge), are bonded in a head-on fashion to the bis-gold chloride fragment, (AuCl)2, and that the structure of Au2-NHSn contains a distorted head-on NHSn ligand, and the NHPb ligand is bonded in a side-on mode to the bis-gold chloride fragment, (AuCl)2. The theoretical calculation of bond dissociation energy (BDE) suggests that the bis-gold chloride-NHEMe bond strength increases from Au2-NHC to Au2-NHSi and then significantly decreases from Au2-NHSi to Au2-NHSn, and the strongest bond is exhibited for Au2-NHPb. The EDA-NOCV results and NOCV pairs indicate that the NHEMe ligand in the Au2-NHE complexes is a strong σ-donor and a weak π-acceptor, as well as a very weak π-donor (AuCl)2←{NHEMe}. The trend in the Au-E bond strength resulted from the increase in (AuCl)2←NHEMe donation. The results of this study may establish an interesting class of compounds worthy of further study.

Bonding analysis of ylidone complexes EL2 (E = C–Pb) with phosphine and carbene ligands L

Quantum chemical calculations using DFT and ab initio methods have been carried out of the compounds EL2 with atoms E = C–Pb and the ligands L = PPh3, N-heterocyclic carbene (NHC), bicyclic NHC, and cyclic alkyl-amino carbene (cAAC). The equilibrium structures are reported and the bonding situation was analyzed with a variety of charge- and energy decomposition methods. Some of the molecules are experimentally known, but most molecules have not yet been prepared. The bonding analysis suggests that all but one molecule should be considered as ylidones that possess dative bonds L→E←L. The sole exception is C(cAAC)2, which has a linear structure and classical double bonds (cAAC)=C=(cAAC). The ylidones EL2 have two lone-pair orbitals at atom E with σ and π symmetry. The π lone pair is somewhat delocalized due to L←E→L π-backdonation. The contribution of L←E→L π-backdonation relative to L→E←L σ-donation increases for the heavier elements. The compounds have rather large first and second proton affinities, which is a characteristic feature of ylidones. They are thus double Lewis bases that could be utilized in chemical reactions.

Clarifying binding difference of ATP and ADP to extracellular signal-regulated kinase 2 by using molecular dynamics simulations.

Extracellular signal-regulated kinase 2 is a promising target for designs and development of anticancer drugs. Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann method were applied to study binding difference of ADP and ATP to extracellular signal-regulated kinase 2. The results prove that the binding ability of ATP to extracellular signal-regulated kinase 2 is stronger than that of ADP. Principal component analysis performed by using molecular dynamics trajectories suggests that binding of ADP and ATP to extracellular signal-regulated kinase 2 change motion directions of two helices α1 and α2. Residue-based free energy decomposition method was adopted to calculate contributions of separate residues to associations of ADP and ATP with extracellular signal-regulated kinase 2. The results show that ADP and ATP produce strong CH-π interactions with five residues Ile29, Val37, Ala50, Leu105, and Leu154. In addition, five hydrogen bonding interactions of ADP and ATP with residues Lys52, Gln103, Asp104, and Met106 also stabilize bindings of ADP and ATP to extracellular signal-regulated kinase 2. Overall, the CH-π interactions of ATP with five residues Ile29, Val37, Ala50, Leu105, and Leu154 are stronger than ADP. This study is expected to contribute a significant theoretical hint for designs of anticancer drugs targeting extracellular signal-regulated kinase 2.

Mor-Dalphos-Pd (II) oxidative addition complexes and related NH3 adducts: Insights into bonding and nonbonding interactions

The stabilizing effects and bonding properties of the Pd metallic center in [(κ2-P,N-Mor-Dalphos)Pd(Ar)Cl] complexes and related NH3 adducts were investigated by density functional theory (DFT), the intrinsic bond orbital (IBO) approach and the Su–Li energy decomposition method (Su–Li EDA). The IBO analysis showed that the P atom from the P,N-Mor-Dalphos structure has stabilizing contributions in all Pd-Cl and Pd-NH3 bonds in the complexes. According to the Su–Li energy decomposition analysis, the main energy that drives the interaction between the [Mor-Dalphos-Pd(Ar)] moiety and Cl− is the electrostatic term, therefore, the electrostatic energy interaction between them might be an important factor for taking into account when designing other [Mor-Dalphos-Pd(Ar)]-Cl precatalysts.

Structures and Bonding Situation of Iron Complexes of Group‐13 Half‐Sandwich ECp* (E = B to Tl) Based on DFT Calculations

AbstractQuantum chemical calculations at the BP86 level with various basis sets (SVP, TZVPP, and TZ2P+) were carried out for the Fe(CO)4 of group‐13 half‐sandwich ECp* [Fe(CO)4‐ECp*] (Fe4‐E) (E = B to Tl). The chemical bonding of the Fe(CO)4‐ECp* bond was analyzed with charge‐ and energy decomposition methods. The calculated equilibrium structures of complexes Fe4‐E show that the ligands ECp* are bonded in an end‐on way to the fragment Fe(CO)4 in Fe4‐E with E = B to Ga. The compound Fe4‐In has a distorted end‐on ligand InCp*. In contrast, Fe4‐Tl has a side‐on bonded ligand TlCp*. The calculated bond dissociation energies (BDEs) suggest that the bond in the iron group‐13 half‐sandwich complexes Fe4‐E decreases from Fe4‐B to Fe4‐Tl. Natural bond orbital (NBO) analysis of the bonding situation reveals that the Fe(CO)4←ECp* donation in Fe4‐E comes from the σ lone‐pair orbital of ECp*. Bonding analysis indicates that the ligand ECp* in complexes are strong σ donors and the NOCV pairs of the bonding show small π‐back donation from the Fe(CO)4 to the ECp* ligands.

Non-Covalent Interactions in Hydrogen Storage Materials LiN(CH3)2BH3 and KN(CH3)2BH3

In the present work, an in-depth, qualitative and quantitative description of non-covalent interactions in the hydrogen storage materials LiN(CH3)2BH3 and KN(CH3)2BH3 was performed by means of the charge and energy decomposition method (ETS-NOCV) as well as the Interacting Quantum Atoms (IQA) approach. It was determined that both crystals are stabilized by electrostatically dominated intra- and intermolecular M∙∙∙H–B interactions (M = Li, K). For LiN(CH3)2BH3 the intramolecular charge transfer appeared (B–H→Li) to be more pronounced compared with the corresponding intermolecular contribution. We clarified for the first time, based on the ETS-NOCV and IQA methods, that homopolar BH∙∙∙HB interactions in LiN(CH3)2BH3 can be considered as destabilizing (due to the dominance of repulsion caused by negatively charged borane units), despite the fact that some charge delocalization within BH∙∙∙HB contacts is enforced (which explains H∙∙∙H bond critical points found from the QTAIM method). Interestingly, quite similar (to BH∙∙∙HB) intermolecular homopolar dihydrogen bonds CH∙∙∙HC appared to significantly stabilize both crystals—the ETS-NOCV scheme allowed us to conclude that CH∙∙∙HC interactions are dispersion dominated, however, the electrostatic and σ/σ*(C–H) charge transfer contributions are also important. These interactions appeared to be more pronounced in KN(CH3)2BH3 compared with LiN(CH3)2BH3.

Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation.

Binding abilities of current inhibitors to MDMX are weaker than to MDM2. Polarizable molecular dynamics simulations (MD) followed by Quantum mechanics/molecular mechanics generalized Born surface area (QM//MM-GBSA) calculations were performed to investigate the binding difference of inhibitors to MDM2 and MDMX. The predicted binding free energies not only agree well with the experimental results, but also show that the decrease in van der Walls interactions of inhibitors with MDMX relative to MDM2 is a main factor of weaker bindings of inhibitors to MDMX. The analyses of dihedral angles based on MD trajectories suggest that the closed conformation formed by the residues M53 and Y99 in MDMX leads to a potential steric clash with inhibitors and prevents inhibitors from arriving in the deep of MDMX binding cleft, which reduces the van der Waals contacts of inhibitors with M53, V92, P95 and L98. The calculated results using the residue-based free energy decomposition method further prove that the interaction strength of inhibitors with M53, V92, P95 and L98 from MDMX are obviously reduced compared to MDM2. We expect that this study can provide significant theoretical guidance for designs of potent dual inhibitors to block the p53-MDM2/MDMX interactions.