Interaction Energy Values Research Articles

Theoretical investigation of vinylogous anomeric effect on 4-halo-4-H-pyran and 4-halo-4-H-thiopyran molecules

ABSTRACTIn this study, the stability of the 4-halo-4-H-pyran and 4-halo-4-H-thiopyran molecules in planar and puckered conformations was investigated in the B3LYP/6-311++G(d,p) level of theory. The total energy, dipole moment, the energies of frontier orbitals, and HOMO–LUMO gaps of the molecules were calculated. Natural bond orbital (NBO) analysis was used to illustrate vinylogous anomeric effect on the puckering of ring. The responsible interactions of this effect were determined. The interaction energy, off-diagonal elements and dipole moment values of their NBO were calculated. In addition, total steric exchange energy values of theses interaction were evaluated.

Extension of the atom by atom scheme of counterpoise method and presentation of its new advantages.

In this paper, for the first time, we want to clearly show that two types of binding energies, cited here as interaction energies (IEs) and stabilization energies (SEs), may need different values of basis set superposition error (BSSE) corrections. We also report the first calculation of the BSSE correction for the strain energies (ES) of supermolecular systems. For this purpose, the known atom by atom scheme of the counterpoise method was extended to mathematically show that the values of BSSE for IE versus SE of a defined system can be really different. Then the IE and SE values of some AB and ABC supermolecules were corrected for BSSE, calculated through the full counterpoise method (CPn) versus its atom by atom scheme (CPaa). The data confirmed that the CPaa accurately gives the different BSSE values for IE versus SE when there is a noticeable difference between the values of these energies. In the above case, the CPn method that gives a single value of BSSE for both IE and SE is not a suitable choice for correcting the SE values.

Density functional theory study of adsorption properties of non-carbon, carbon and functionalized graphene surfaces towards the zinc and lead atoms

In the current study, we Investigated the adsorption properties of zinc (Zn) and lead (Pb) atoms on the surface of carbonic and non-carbonic graphene using Density functional theory calculations. The procedure for this research can be divided into two sections. First, we calculated the adsorption value of single zinc and lead atoms with such non-carbonic graphene-like structures as Boron-Nitride (BN), Aluminum-Nitride (AlN), Gallium-Nitride (GaN), Silicon-Carbide (SiC), and Silicene. We found that the silicene was more powerful to detect the stated heavy metal atoms compared with others. The calculated adsorption values between the single zinc and lead atoms with silicene monolayer sheet were equal to −0.90 eV and −3.80 eV, respectively. We also used electron transfer calculations after adsorbing the stated heavy metal atoms and found that the calculated charge transfer was equal to 0.42 and 0.12 electrons for Silicene/Pb and Silicene/Zn complex, respectively. The density of states (DOS) results demonstrated that a strong hybridization could occur between the Pb atom and the silicene graphene. Then, we performed DFT calculations to determine the interaction energy between the mentioned metal atoms with pristine carbonic graphene. We found that the interaction in graphene/Zn (−0.09 eV) and graphene/Pb (−0.45 eV) was so weak, especially for graphene and zinc. To overcome this issue, we first activated the surface of graphene by carboxyl and hydroxide group. The interaction energy values between the zinc and lead atoms with graphene-COOH were approximately −0.18 eV and −1.01 eV, respectively, which showed improvements in the adsorption energy. Then, we approached the mentioned metal atoms on the surface of OH-decorated graphene and demonstrated that the interaction energy between the single zinc and lead atoms with graphene-OH were about −0.78 eV and −3.33 eV. In other words, it improved by 755% and 623% compared with graphene/Zn and graphene/Pb, respectively. The strong adsorption between the hydroxyl group and the stated metals atom caused the OH group to be isolated from the graphene surface and become an individual molecule.

Binuclear mercury (II) complexes of ambidentate sulfonium ylides in comparison with analogous phosphonium-based complexes; synthesis, characterization and a comprehensive theoretical study

The dehydrobromination reaction of a new sulfonium salt [(Me)2SCH2(O)C10H7]Br (1) with sodium hydroxide solution led to formation of sulfonium ylide (Me)2SCHC(O)C10H7 (2) which was used to synthesize three binuclear complexes [{(Me)2SCHC(O)C10H7}2HgX2]2 (X = Cl (3), Br (4) and I (5)). Characterization of all compounds was thoroughly performed by elemental analysis, IR, 1H and 13C NMR spectroscopic methods. Also the structure of complex (4) was characterized by X-ray crystalography methode. The structure of prepared complexes was also compared with analogous phosphonium complexes [{Ph3PCHC(O)C10H7}2HgX2]2 (X = Cl, Br and I) using DFT calculations with the M06/def2-SVP level of theory. Based on the theoretical studies of geometry-optimized bidentate structures, the interaction energy values, ΔEint, for C→M bonds in [{(Me)2SCHCOC10H7}HgX2]2 complexes are larger than those in [{Ph3PCHCOC10H7}HgX2]2 (X = Cl, Br and I) complexes. Obviously, in comparison to the phosphonium ylide, the sulfonium ylide forms a stronger bond with Hg2X4 (X = Cl, Br and I) fragments in aforementioned complexes.

Studies on the UV filtering and radical scavenging capacity of the bitter masking flavanone Eriodictyol

A computational analysis of UV filtering and radical scavenging capacity of a flavanone, Eriodictyol has been performed under DFT-B3LYP/6–31+ G (d, p). Eriodictyol is nontoxic and nonirritant bitter masker commonly used in the wine industry. It has been reported that the flavanones were widely acceptable for photoprotection due to its potential UV filtering and radical scavenging capacity. This study provides theoretical evidence that the eriodictyol has an absorbance in the UV-A and UV-B region of the electromagnetic spectrum and therefore can be used as a potential UV filter in sunscreen lotions and other cosmetic products. The major transitions in the UV–Visible spectrum of Eriodictyol are between HOMO and HOMO-1 with LUMO level and are well explained by NBO-NLMO tool in G09 software. In addition to this, Eriodictyol is a potent antioxidant than that of the most commonly studied Quercetin. The most active site in the compound is 3′ position and is confirmed by NPA, NBO and pKa value analysis. The lowest energy conformer of Eriodictyol contains a Hydrogen bond between carbonyl oxygen (O2) and H30. This is confirmed by the highest value of interaction energy between lone pairs of O2 and σ* of O3– H30. Both the two lone pairs of O2 interacts with the σ* of O3-H30. This decreases the bond order of 5 OH and at the same time it restricts the hydrogen transfer from this position to form a radical. Similarly, the lone pair of O5 (3′ position) interacts with H33 resulting in the low bond order value and consequently less favorable for radical formation. These results indicate that the BDE values follow the order 3′ < 4′ < 7 < 5. Thus the title compound can be used for photo protection due to its potential UV filtering and radical scavenging capacity.

Interaction energy profile for diphenyl diselenide in complex with δ-aminolevulinic acid dehydratase enzyme using quantum calculations and a molecular fragmentation method

Studies has pointed out the selenocompound diphenyl diselenide [(PhSe)2] as a novel promising drug with antioxidant, neuroprotective, anti-atherosclerotic and anti-inflammatory effects. In the opposite way, (PhSe)2 can also present cytotoxic properties and inhibit the activity of δ-aminolevulinic acid dehydratase (δALAD) and other thiol-containing proteins. δALAD inhibition can impair heme biosynthesis and, consequently, affect the aerobic metabolism. In order to deepen the analysis of the molecular mechanisms concerning δALAD inhibition by (PhSe)2, we performed theoretical quantum calculations within the Density Functional Theory (DFT) approach related to the interaction energies between amino acid residues and (PhSe)2 via Molecular Fragmentation with Conjugated Caps (MFCC) method. The quantum calculations revealed that interactions between (PhSe)2 moieties and δALAD could occur up to 9 Å distance from the (PhSe)2 active site centroid located inside the TIM barrel active site of δALAD. In addition, Phe208, Phe79, Cys122, Cys124, Pro125, Asp120, Lys199, Lys252, and Cys132 presented stronger attractive interaction energies to (PhSe)2 than to other closer residues and could be pointed out as essential for complex stability (interaction energy values ranging from −23.75 kcal·mol−1 to −11.74 kcal·mol−1 for DFT LDA/PWC and from −19.75 kcal·mol−1 to −6.76 kcal·mol−1 for DFT GGA/PW91). The analysis of the calculated energy values and the electrostatic potential together clarify that the two phenyl moieties in (PhSe)2 are key players in strongly attracting to aromatic, hydrophobic, and positively charged side chains from residues of the δALAD active site. Consequently, the spatial orientation assumed by (PhSe)2 allows the electrophile moiety Se-Se closer to thiolate groups of catalytic Cys122, Cys124, and Cys132, leading to consequent thiol oxidation and zinc release. In conclusion, these pieces of information may improve the previous understanding of the molecular docking model and could be useful to guide future studies concerning the rational design of novel diselenide-derived drugs with low affinity for δALAD.

7-Hexyloxy-3-[4’-(3-methylbutyloxy) phenyl]-4H-1-benzopyran-4-one: Study of Smectic behaviour and UV absorption profile

abstractThe intermolecular interaction energies between a pair of 7-Hexyloxy-3-[4’-(3-methylbutyloxy) phenyl]-4H-1-benzopyran-4-one (HMBPB) molecules have been estimated with respect to translational and orientational motions. The complete neglect differential overlap (CNDO/S) method has been employed to calculate the net atomic charge and atomic dipole moment components at each atomic center. The modified Rayleigh-Schrodinger perturbation theory along with multicentered-multipole expansion method has been employed to evaluate the long-range intermolecular interactions, while a ‘6-exp’ potential function has been assumed for short-range interactions. The total interaction energy values obtained through these computations have been used to calculate the probability of each configuration at room temperature (300K), and isotropic-smectic transition temperature (412.6K). Molecular arrangements inside a bulk of materials and smectic behavior of the compound in terms of their relative order have been discussed. Translational and rotational rigidity of the molecule has been analyzed to understand the smectic behaviour. The UV absorption profile has been estimated using CNDO/S, and INDO/S methods.

Structural, spectroscopic and thermodynamic aspects of azide–water clusters: an approach using a conjugated prescription of stochastic and quantum chemical methods

ABSTRACTIn this work, we have used the stochastic search strategy of adaptive mutation simulated annealing (AMSA) as the search tool to explore quantum chemical potential energy to find structures for clusters for n up to 8. The evaluated structures are then further refined at higher levels of theories to get more accurate values of IR frequencies, interaction energy (IE), solvation energy (SE) and vertical detachment energy (VDE). The variations of IE, SE and VDE are also observed and critically discussed to understand the observed trends and their correspondence with experimental findings. In a real experimental scenario, where finite temperature is present, any obtained property will be dictated by contribution from local isomers along with the global one. Keeping this important fact in mind, we have investigated conformational populations of different isomers for the atmospherically relevant temperature range between 200 K and 300 K.

The possibility of iron chelation therapy in the presence of different HPOs; a molecular approach to the non-covalent interactions and binding energies

Nowadays, 3-hydroxypyridine-4-ones (HPOs) as orally active iron chelators have been introduced for the treatment of disorders associated with iron such as iron overload in thalassemia patients. In this work, a density functional theory (DFT) study was performed on a series of HPOs constituted of the different substitutions at the different positions. Structural analysis indicates that all of the HPO derivatives bind to Fe3+ as a two-dentate mode through the oxygen atoms of the C=O groups. It is confirmed that the HPO derivative composed of three methyl groups at the different positions (3-hydroxy-1,2,5-trimethyl-4(1H) pyridinone) forms the most stable complex with Fe3+. Therefore, this HPO derivative acts as a better iron chelator than other ones. The vibrational frequency analysis reveals a correlation between the iron affinity constant and C=O vibrational frequency of the HPOs. Donor-acceptor interactions show an effective charge transfer from the oxygen atoms of the HPOs towards Fe3+. Quantum theory of atoms in molecules analysis shows the non-covalent interactions, mainly, electrostatic interactions play an important role in the complex formation of the HPOs and Fe3+. Finally, some linear correlations between the electron densities of the Fe−O chemical bond and interaction energy values, the vibrational frequency of the C=O bonds and electron densities of the Fe−O chemical bond were obtained and analyzed.

Formation and autocatalytic nucleation of co-zone [formula omitted] deformation twins in polycrystalline Mg: A phase field simulation study

A phase-field model is developed to study the formation and autocatalytic nucleation of {101¯2} twins in polycrystalline Mg. The twins are found to nucleate most favourably in grains with the most negative interaction energy. Within such grains, the energetically most favoured nucleation site is determined by stresses concentrated near the grain boundaries that are related to the elastic anisotropy of the material. Furthermore, in a structure consisting of three lamellar grains with an incoming twin in the central grain, the simulation results show that before autocatalytic nucleation, the incoming twin often has a lenticular shape. The stress field around the tip of the incoming twin plays the major role in the autocatalytic nucleation. After a twin has nucleated in the neighbouring grain, the incoming and the outgoing twins evolve simultaneously, and the shape of the incoming twin gradually changes from lenticular to parallel-sided plate. Under the condition that the crystallographic orientation of the central grain and the applied strain remains unchanged, the driving force for twin nucleation decreases with increasing misorientation (up to 90°) across the grain boundary. It is further derived that the interaction energy values between the pre-existing stress field of the polycrystalline structure and the eigenstrain of the to-be-nucleated twin is mathematically related to the resolved shear stress of twins.

Strength of π-Stacking, from Neutral to Cation: Precision Measurement of Binding Energies in an Isolated π-Stacked Dimer.

π-Stacking interactions are ubiquitious across chemistry and biochemistry, impacting areas from organic materials and photovoltaics to biochemistry and DNA. However, experimental data is lacking regarding the strength of π-stacking forces-an issue not settled even for the simplest model system, the isolated benzene dimer. Here, we use two-color appearance potential measurements to determine the binding energies of the isolated, π-stacked dimer of fluorene (C13H10) in ground, excited, and ionic states. Our measurements provide the first precise values for π-stacking interaction energies in these states, which are key benchmarks for theory. Indeed, theoretical predictions using ab initio and carefully benchmarked DFT methods are in excellent agreement with experiment.

Cytochrome P450 2C9-natural antiarthritic interactions: Evaluation of inhibition magnitude and prediction from in vitro data.

Many dietary supplements are promoted to patients with osteoarthritis (OA) including the three naturally derived compounds, glucosamine, chondroitin and diacerein. Despite their wide spread use, research on interaction of these antiarthritic compounds with human hepatic cytochrome P450 (CYP) enzymes is limited. This study aimed to examine the modulatory effects of these compounds on CYP2C9, a major CYP isoform, using in vitro biochemical assay and in silico models. Utilizing valsartan hydroxylase assay as probe, all forms of glucosamine and chondroitin exhibited IC50 values beyond 1000μM, indicating very weak potential in inhibiting CYP2C9. In silico docking postulated no interaction with CYP2C9 for chondroitin and weak bonding for glucosamine. On the other hand, diacerein exhibited mixed-type inhibition with IC50 value of 32.23μM and Ki value of 30.80μM, indicating moderately weak inhibition. Diacerein's main metabolite, rhein, demonstrated the same mode of inhibition as diacerein but stronger potency, with IC50 of 6.08μM and Ki of 1.16μM. The docking of both compounds acquired lower CDOCKER interaction energy values, with interactions dominated by hydrogen and hydrophobic bondings. The ranking with respect to inhibition potency for the investigated compounds was generally the same in both in vitro enzyme assay and in silico modeling with order of potency being diacerein/rhein > various glucosamine/chondroitin forms. In vitro-in vivo extrapolation of inhibition kinetics (using 1 + [I]/Ki ratio) demonstrated negligible potential of diacerein to cause interaction in vivo, whereas rhein was predicted to cause in vivo interaction, suggesting potential interaction risk with the CYP2C9 drug substrates.

Novel 2-pheynlbenzofuran derivatives as selective butyrylcholinesterase inhibitors for Alzheimer\u2019s disease

Alzheimer’s disease (AD) is a neurodegenerative disorder representing the leading cause of dementia and is affecting nearly 44 million people worldwide. AD is characterized by a progressive decline in acetylcholine levels in the cholinergic systems, which results in severe memory loss and cognitive impairments. Expression levels and activity of butyrylcholinesterase (BChE) enzyme has been noted to increase significantly in the late stages of AD, thus making it a viable drug target. A series of hydroxylated 2-phenylbenzofurans compounds were designed, synthesized and their inhibitory activities toward acetylcholinesterase (AChE) and BChE enzymes were evaluated. Two compounds (15 and 17) displayed higher inhibitory activity towards BChE with IC50 values of 6.23 μM and 3.57 μM, and a good antioxidant activity with EC50 values 14.9 μM and 16.7 μM, respectively. The same compounds further exhibited selective inhibitory activity against BChE over AChE. Computational studies were used to compare protein-binding pockets and evaluate the interaction fingerprints of the compound. Molecular simulations showed a conserved protein residue interaction network between the compounds, resulting in similar interaction energy values. Thus, combination of biochemical and computational approaches could represent rational guidelines for further structural modification of these hydroxy-benzofuran derivatives as future drugs for treatment of AD.

DFT/TD-DFT study on the electronic and spectroscopic properties of hollow cubic and hollow spherical (ZnO) m quantum dots interacting with CO, NO2 and SO3 molecules

Hollow spherical (HS) and hollow cubic (HC) (ZnO) m quantum dots (QDs) were constructed and optimized using density functional theory (DFT) method. CO, NO2 and SO3 molecules were used to interact with the HC and HS (ZnO) m QDs at the centre and on the surface of the QDs. The changes in the electronic energy levels of HC and HS (ZnO) m QDs due to the interactions of CO, NO2 and SO3 molecules have been studied. The electronic and spectroscopic properties, such as density of states, HOMO–LUMO energy gap, absorption spectra, IR and Raman spectra of HC and HS (ZnO) m QDs have been studied using DFT and Time dependent-DFT (TD-DFT) methods. The interaction energy values show that the SO3 molecule has strongly interacted with HC and HS (ZnO) m QDs than the CO and NO2 molecules. The results of the density of states show that the HC QDs have peaks that are very close to each other, whereas the same is found to be broad in the HS QDs. The HOMO–LUMO energy gap is more for the HS QDs than the HC QDs, and also it gets decreased, when the NO2 and SO3 molecules interact at the centre of the HC and HS (ZnO) m QDs. The blue and red shifts were observed in the absorption spectra of HS and HC QDs. The natural transition orbital (NTO) plot reveals that the interaction of the molecules on the surface of the QDs reduce the chance of electron–hole recombination; hence the energy gap increases for NO2 and SO3 molecular interactions on the surface of the HC and HS (ZnO) m QDs. The vibrational assignments have been made for HC and HS QDs interacting with CO, NO2 and SO3 molecules.

Synthesis and Pain Inhibition Activity of the Analogs of 1-Allyl-3-Benzoylthiourea for New Analgesic Lead Compound Discovery

Objective: The study aimed to synthesize four analogs of 1-allyl-3-benzoylthiourea (R= H; 2-Cl; 3-Cl; and 4-Cl), and evaluate their pain inhibition activities. Method: The chemical structure was drawn assisted by Chem- Draw Ultra 8.0 and Chem3D Ultra 8.0 software. Molegro Virtual Docker 5.0 software was utilized for the docking process, to determine the interaction energy values between compounds of interest and the COX-2 receptor (PDB: 1PXX). The synthesis step was done by nucleophilic substitution (benzoylation) on allylthiourea compound via modified Schotten-Baumann reaction. Chemical structure analysis was evaluated by means of Infra-Red, Nuclear Magnetic Resonance, and Mass Spectroscopy methods. The pain inhibition assay was done using acetic acid induced writhing test, using mice (Mus musculus) as animal model. Results: Preliminary in silico screening showed that all four candidate compounds possessed good interaction on COX-2 receptor. The synthesis process produced rendemen of the compounds vary between 15.2 %-47%. Chemical structure evaluation confirmed the structural match of the products as expected. Acetic acid induced writhing test in mice (Mus musculus) showed that three compounds possessed a better pain inhibition activity compared to positive control diclofenac sodium. Conclusion: 1-allyl-3-benzoylthiourea analogs showed good pain inhibition activity. The compounds can serve as leads for analgesic activity through the inhibition of COX-2. Key words: Synthesis, 1-allyl-3-benzoylthiourea, COX-2, Analgesic, Lead Compound.

Improvement of Anion Transport Systems by Modulation of Chalcogen Interactions: The influence of solvent.

A series of potential anion transporters, dithieno[3,2-b;2',3'-d]thiophenes (DTT), involving anion-chalcogen interactions have been studied by analyzing the interaction energy, geometry, and charge transfer. It was found that gas phase calculations show very negative interaction energies with short anion-chalcogen distances, but when solvent effects are considered, the interaction energy values decreased drastically concomitantly with an elongation on the interatomic distances. To enhance the chalcogen interaction between the DTT derivatives and the anion, increasing the anion transporter capacity, bisisothioazole moiety was considered; i.e., the σ-hole of the chalcogen atom was modulated by substitution of the adjacent carbon by a nitrogen atom in the S-C axis, increasing the depth of the σ-hole and therefore the interaction between the chalcogen and anion. Finally, different anions were analyzed within the complexes, finding that F- and NO3- would be the best candidates to form complexes and possibly displace other anions such as Cl- or Br-.

Ionic liquid based on 6‐amino‐6‐deoxy hexopyranose cation and BF4¯, PF6¯, and ClO4¯ as anions: A DFT study on the structural and electronic properties

AbstractIn this study, the structural and electronic properties of a carbohydrate‐based (6‐amino‐6‐deoxy hexopyranose [ADHP]) ionic liquid were explored. The interactions among 3 anions (BF4¯, PF6¯, and ClO4¯) and ADHP as cation were investigated at B3LYP/6‐311++G(d,p) level. Based on the calculated interaction energy, it was found that PF6¯ anion has the highest interaction energy with ADHP. It was found that the hydrogen bonds play an important role in the interaction of ion pairs. The nature of hydrogen bonds in the optimized ion pars was analyzed by using natural bond orbital analysis and the quantum theory of atoms in molecules. The linear relationship between electron density at the bond critical points of hydrogen bonds and the interaction energy values was checked.

A new approach to precise thermodynamic characterization of hybridization properties of modified oligonucleotides: Comparative studies of deoxyribo- and glycine morpholine pentaadenines

The development of new derivatives and analogues of nucleic acids for the purposes of molecular biology, biotechnology, gene diagnostics, and medicine has been a hotspot for the last two decades. Methylenecarboxamide (glycine) morpholine oligomer analogues (gM) seem to be promising therapeutic candidates because of the ability to form sequence specific complexes with DNA and RNA. In this paper we describe new approaches to the determination of thermodynamic parameters for hybridization of tandem oligonucleotide complexes with the complementary template. It makes possible to determine changes in enthalpy and entropy corresponding to the binding of an individual oligomer with the template, and to the formation of cooperative contact at the helix-helix interface of two neighboring duplex fragments (in the nick). We have experimentally analyzed the series of model tandem complexes of different length at various oligomer concentrations, ionic strength, and pH. The analysis of thermodynamic parameters of complex formation for native and modified oligomers revealed higher Gibbs free energy values of hybridization and cooperative interaction of morpholine-containing complexes at the helix-helix interface under standard conditions (1M NaCl, pH7.2). Further comparative analysis of the hybridization properties of modified oligomers at ionic strength and pH allows us to determine the charge state of the morpholine backbone and the thermodynamic origin of the effects observed. It was found that the decrease in pH to 5.5 led to the protonation of internal morpholine nitrogens. The obtained results prove the veracity of the proposed model and the possibility to evaluate thermodynamic parameters of short native and modified oligomers with high accuracy.

In Silico Chromatography: Modeling a New Support for Alkyl-Bonded Phases and a Solvent Phase

Chromatography is a tool to measure molecular interactions, and computational chemistry is a tool to explain molecular interactions. Therefore, reversed-phase liquid chromatography of acidic drugs using a pentyl- and an octyl-bonded silica gels was quantitatively analyzed in silico. A model pentyl- and an octyl-bonded silica gel and a methanol phases were constructed for docking with acidic drugs. Molecular interaction energy values based on van der Waals energy were obtained after docking an acidic drug into the model pentyl- or octyl-phases. Solvent effects, hydrogen bonding, and electrostatic energy values were obtained after docking an acidic drug onto the model methanol phase. Chromatographically measured log k values were correlated with the sum of van der Waals, hydrogen bonding, and electrostatic energy values. The correlation coefficient between the log k values measured using the pentyl-bonded silica gel phase and the molecular interaction energy values was 0.95 (n = 20); that between the log k values measured using the octyl-bonded silica gel and the molecular interaction energy values was 0.95 (n = 20).

Quantitative Explanation of Retention Mechanisms of Hydrophobic and Hydrophilic-Interaction Liquid Chromatography-Inductive Effect of Alkyl Chain

The basic retention mechanisms of reversed-phase and hydrophilic-interaction liquid chromatography (HILIC) were quantitatively analyzed using simple molecular mechanics (MM) calculations. The model bonded phases were composed of an alkyl chain bonded to siloxane-like molecules. The head of the alkyl chain was a hydroxyl group, used to study retention mechanisms of HILIC. The standard analytes were benzoic acid, aniline, benzene, water, and acetonitrile. The molecular interaction (MI) energy values of the van der Waals (VW) force were predominant for the reversed-phase chromatography, and those of hydrogen bonding (HB) were predominant for HILIC. Up to 5 units of methylene affected the MI.