A comparison of methods to compute the potential of mean force.

Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is determined, this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane molecules in aqueous solution. We analyze all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from density of states or force averaging) and the type of coordinate system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Theoretical study of the adsorption of oxygen on a Cu(100) surface and the coadsorption with alkali atoms

We performed a theoretical study of the adsorption of oxygen on a cluster model of the Cu(100) surface and also the surface coadsorbed with lithium and potassium atoms. The study showed that alkali coadsorption facilitates in a significant way the process of molecular adsorption, whereas the adsorption of atomic oxygen is only slightly modified. The alkali atoms on the copper surface produce an increase in the charge transfer toward the oxygen molecule, favoring the oxygen dissociation. The effect is greater for the potassium coadsorption. In addition, we found that the potassium coadsorption favored the dissociation and recombination processes by about 60 and 15%, respectively. In turn, the lithium coadsorption favored only the recombination process by about 50%. These results could be an important aspect for catalytic processes.From the Proceedings of the 28th Congreso de Quimicos Teóricos de Expression Latina (QUITEL 2002)     

Theoretical study of Sn adsorbed on the MgO(100) surface with defects

In this study, the adsorption of Sn atom at various sites on the MgO(100) surface was characterized using a theoretical approach based on density functional theory calculations. Both regular adsorption centers (O^2? and Mg²⁺) and defects (such as neutral and charged O and Mg vacancies) were considered. Several key parameters for these sites with the adsorbed Sn atom were determined to provide its geometric, energetic, and electronic characterization. The interaction between Sn and the Mg vacancy sites is very strong and is associated with a relatively small distance of the adsorbed Sn atom from the surface and with a large electronic charge transfer from Sn to the surface. A much smaller strength of Sn atom adsorption is observed for the O vacancies and regular sites. Among them, the ${{\text{F}}_{\text{s}}}^{\text{0}}$ center binds the Sn atom strongest and, in consequence, this atom acquires a significant amount of electronic charge.     

DOPA醌在Cu(100)表面吸附的密度泛函理论研究

采用广义梯度密度泛函理论(GGA)的BLYP方法结合周期性平板模型,以原子簇Cu41为模拟表面,对DOPA醌分子在Cu(100)表面不同位置的吸附模型进行了构型优化、能量计算以及Mulliken布居分析,结果表明通过相邻的羰基垂直吸附在表面的桥位是其最佳吸附方式,吸附能为247.2310kJ/mol;其次为顶位、顶位R45和穴位,吸附能分别为227.7162kJ/mol、220.7305kJ/mol和217.8456kJ/mol。Mulliken布居分析结果表明整个吸附体系发生了由Cu原子向DOPA醌分子的电荷转移。     

Effects of coverage and solvent on H2S adsorption on the Cu(100) surface: A DFT study

Density functional theory is used to investigate the effects of coverage and solvent on the adsorption of H₂S on the Cu(100) surface. In this work, the adsorption energies, structural parameters and Mulliken charges of the adsorbed H₂S are calculated. The results show that when the coverage of H₂S is high (1 ML), H₂S molecule cannot adsorb on the Cu(100) surface spontaneously, and the decomposition of H₂S preferentially occurs at the bridge site. When the coverage decreases to 1/4 ML coverage, H₂S molecule does not exhibit the decomposition, but bonds to the top Cu atom with the tilted adsorption. Furthermore, when the coverage is 1/9, 1/16 and 1/25 ML, H₂S adsorption remains stable. In addition, the stability of H₂S adsorption on the Cu(100) surface improves rapidly when the solvent dielectric constant (ε) increases from 1 to 12.3 corresponding to the vacuum and pyridine, respectively. For the higher ε (≥24.3), the effect of the solvent on the H₂S adsorption was greatly reduced. In this work, both coverage and solvent are shown to have an important effect on the H₂S adsorption on the Cu(100) surface, which might be useful to improve the future similar simulations. Copyright © 2015 John Wiley & Sons, Ltd.     

Density functional theory for adsorption of HCHO on the FeO（100） surface

The density functional theory (DFT) and periodic slab model were used to get information concerning the adsorption of HCHO on the FeO(100) surface. A preferred η2-(C,O)-di-σ four-membered ring adsorption conformation on the Fe-top site was found to be the most favorable structure with the predicted adsorption energy of 210.7 kJ/mol. The analysis of density of states, Mulliken population, and vibrational frequencies before and after adsorption showed clear weakening of the carbonyl bond, and high sp3 charact...     

Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks

Summary: Reinforcement of elastomers is modeled using Monte Carlo simulations on rotational isomeric state chains, to characterize their spatial configurations in the vicinity of filler particles. The resulting filler-perturbed distributions of the chain end-to-end distances are in agreement with experimental results gotten by neutron scattering. The use of these distributions in a standard molecular theory of rubberlike elasticity produces stress-strain isotherms for elongation that are consistent with available experimental results.     

First-principles study of the adsorption of formaldehyde on the clean and atomic oxygen covered Cu(1 1 1) surface

The interaction of formaldehyde with the clean and atomic oxygen-covered Cu(1 1 1) surfaces has been studied by means of cluster model density functional calculations in which Cu₂₂(14,8) is used to represent the perfect Cu(1 1 1) surface. The calculations point towards a η¹-H₂CO---O orientation with the oxygen atom almost on top of a copper surface atom. The formaldehyde adsorption energy is of 22–25 kJ/mol and the internal geometry of adsorbed formaldehyde is almost identical to that of the molecule in the gas-phase. The C---O bond is almost parallel to the surface and the conformation with the molecular plane normal to the surface is slightly preferred to the conformation with the molecular plane nearly parallel to the surface. A Cu₂₂---O model where atomic oxygen is adsorbed on a fcc hollow site was used to study the co-adsorption and reaction of formaldehyde with atomic oxygen. Oxygen co-adsorption has a dramatic effect on the formaldehyde adsorption energy which is increased by 50%. The calculated energy barrier for the formation of the dioxymethylene intermediate species through the H₂CO+O→H₂CO₂ reaction is of 36 kJ/mol.     

Density functional embedded cluster study of Cu(4), Ag(4) and Au(4) species interacting with oxygen vacancies on the MgO(001) surface

Cu(4), Ag(4), and Au(4) species adsorbed on an MgO(001) surface that exhibits neutral (F(s)) and charged (F(s) (+)) oxygen vacancies have been studied using a density functional approach and advanced embedding models. The gas-phase rhombic-planar structure of the coinage metal tetramers is only moderately affected by adsorption. In the most stable surface configuration, the plane of the tetramers is oriented perpendicular to the MgO(001) surface; one metal atom is attached to an oxygen vacancy and another one is bound to a nearby surface oxygen anion. A very similar structural motif was recently found on defect-free MgO(001), where two O(2-) ions serve as adsorption sites. Following the trend of the interactions with the regular MgO(001) surface, Au(4) and Cu(4) bind substantially stronger to F(s) and F(s) (+) sites than Ag(4). This stronger adsorption interaction at oxygen vacancies, in particular at F(s), is partly due to a notable accumulation of electron density on the adsorbates. We also examined the propensity of small supported metal species to aggregate to adsorbed di-, tri- and tetramers. Furthermore, we demonstrated that core-level ionization potentials offer the possibility for detecting experimentally supported metal tetramers and characterizing them structurally with the help of calculated data.     

Adsorption Sequence of Multifunctional Groups: A Study on the Reaction Pathway and the Adsorption Structure of Homocysteine on the Ge(100) Surface

We investigated the adsorption mechanism of homocysteine (HS? CH₂? CH₂? CH(NH₂)? COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid′s functional groups using core‐level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” and the “SH‐dissociated OH‐dissociation‐bonded structure” were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The “SH‐dissociated OH‐dissociated N‐dative‐bonded structure” was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (? SH), carboxyl group (? COOH), and amine group (? NH₂).     

Density Functional Theory Study on the Adsorption of HCNH and CNH2 on Cu（100） Surface

The HCNH and CNH2 adsorption on different coordination sites of Cu（100） was theoretically studied considering the cluster approach. The present calculations show that the bridge site is the most favorite for CNH2 perpendicularly adsorbed on the Cu（100） surface via the C atom. For HCNH absorbed on the Cu（100） surface, the parallel adsorption mode with the C and N atoms nearly directly above the adjacent top sites of Cu（100） surface is the most favored. Both CNH2 and HCNH are strongly bound to the Cu（100） surface with CNH2 which is lightly stable （2.51 kJ·mol^-1）, indicating that both species may be co-adsorbed on the Cu（100） surface.     

A DFT study of the adsorption and dissociation of CO on Fe(100): influence of surface coverage on the nature of accessible adsorption states.

In the present article, we report adsorption energies, structures, and vibrational frequencies of CO on Fe(100) for several adsorption states and at three surface coverages. We have performed a full analysis of the vibrational frequencies of CO, thus determining what structures are stable adsorption states and characterizing the transition-state structure for CO dissociation. We have calculated the activation energy of dissociation of CO at 0.25 ML (ML = monolayers) as well as at 0.5 ML; we have studied the dissociation at 0.5 ML to quantify the destabilization effect on the CO(alpha3) molecules when a neighboring CO molecule dissociates. In addition, it is shown that the number and nature of likely adsorption states is coverage dependent. Evidence is presented that shows that the CO molecule adsorbs on Fe(100) at fourfold hollow sites with the molecular axis tilted away from the surface normal by 51.0 degrees. The asorprton energy of the CO molecule is -2.54 eV and the C-O stretching frequency is 1156 cm(-1). This adsorption state corresponds to the alpha3 molecular desorption state reported in temperature programmed desorption (TPD) experiments. However, the activation energy of dissociation of CO(alpha3) molecules at 0.25 ML is only 1.11 eV (approximately 25.60 kcal mol(-1)) and the gain in energy is -1.17 eV; thus, the dissociation of CO is largely favored at low coverages. The activation energy of dissociation of CO at 0.5 ML is 1.18 eV (approximately 27.21 kcal mol(-1)), very similar to that calculated at 0.25 ML. However, the dissociation reaction at 0.5 ML is slightly endothermic, with a total change in energy of 0.10 eV Consequently, molecular adsorption is stabilized with respect to CO dissociation when the CO coverage is increased from 0.25 to 0.5 ML.     

Solid-state static Cu and P CP/MAS NMR, and liquid-state EXAFS studies on copper(I) O,O′-dialkyldithiophosphate cluster compounds: Formation of the copper(I) O,O′-di-iso-amyldithiophosphate cluster compound on the surface of synthetic chalcocite

Polycrystalline octa-nuclear copper(I) O,O′-di-i-propyl- and O,O′-di-i-amyldithiophosphate cluster compounds, {Cu₈[S₂P(OR)₂]₆(μ₈-S)} where R = ⁱPr and ⁱAm, were synthesized and characterized by ³¹P CP/MAS NMR at 8.46 T and static ⁶⁵Cu NMR at multiple magnetic field strengths (7.05, 9.4 and 14.1 T). The symmetries of the electronic environments around the P sites were estimated from the ³¹P chemical shift anisotropy (CSA) parameters, δ_aniso and η. Analyses of the ⁶⁵Cu chemical shift and quadrupolar splitting parameters for these compounds are presented with the data being compared to those for the analogous octa-nuclear cluster compounds with R = ⁿBu and ⁱBu. The ⁶⁵Cu transverse relaxation for the copper sites in {Cu₈[S₂P(OⁱPr)₂]₆(μ₈-S)} and {Cu₈[S₂P(OⁱAm)₂]₆(μ₈-S)} was found to be very different, with a relaxation time, T₂, of 590 μs (Gaussian) and 90 μs (exponential), respectively. The structures of {Cu₄[S₂P(OⁱPr)₂]₄} and {Cu₈[S₂P(OⁱPr)₂]₆(μ₈-S)} cluster compounds in the liquid- and the solid-state were studied by Cu K-edge EXAFS. The disulfide, [S₂P(OⁱAm)₂]₂, was obtained and characterized by ³¹P{¹H} NMR. The interactions of the disulfide and of the potassium O,O′-di-i-amyldithiophosphate salt with the surfaces of synthetic chalcocite (Cu₂S) were probed using solid-state ³¹P NMR spectroscopy and only the presence of copper(I) dithiophosphate species with the {Cu₈[S₂P(OⁱAm)₂]₆(μ₈-S)} structure was observed.     

Density Functional Theory Study on the Adsorption of CN on Transition Metal M（100） （M = Ni,Pd, Pt,Cu, Ag and Au） Surfaces

The adsorption of cyanide on the top site of a series of transition metal M（100） （M = Cu, Ag, Au, Ni, Pd, Pt） surfaces via carbon and nitrogen atoms respectively, with the CN axis perpendicular to the surface, has been studied by means of density functional theory and cluster model. Geometry, adsorption energy and vibrational frequencies have been determined, and the present calculations show that the adsorption of CN through C-end on metal surface is more favorable than that via N-end for the same surface. The vibrational frequencies of CN for C-down configuration on surface are blue-shifted with respect to the free CN, which is contrary to the change of vibrational frequencies when CN is adsorbed by N-down structure. Furthermore, the charge transfer from surface to CN causes the increase of surface work function.     

Ab‐Initio calculations of the CO adsorption and dissociation on substitutional Fe–Cu surface alloys relevant to Fischer–Tropsch Synthesis: bcc‐(Cu)Fe(100) and fcc‐(Fe)Cu(100)

Direct CO dissociation is seen the main path of the first step in the Fischer–Tropsch Synthesis (FTS) on the reactive iron surfaces. Cu/Fe alloy film is addressed with various applications over face‐centered‐cubic (fcc)‐Cu and body‐centered‐cubic (bcc)‐Fe in the FTS, i.e. preventing iron carbide formation (through direct CO dissociation) by moderating the surface reactivity and facilitating the reduction of iron surfaces, respectively. In this study by density functional theory, the stable configurations of CO molecule on various Cu/Fe alloys over fcc‐Cu(100) and bcc‐Fe(100) surfaces with different CO coverage (25% and 50%) have been evaluated. Our results showed that the ensemble effect plays a fundamental role to CO adsorption energy on the surface alloys over bcc‐Fe(100); on the other hand, the ligand effect determines the CO stability on the fcc‐Cu(100) surface alloys. CO dissociation barrier was also calculated on the surface alloys that showed although the CO dissociation process is thermodynamically possible on the more reactive surface alloys, but according to their high barrier, CO dissociation does not occur directly on these surfaces. Copyright © 2013 John Wiley & Sons, Ltd.     

The effect of iron and copper impurities on the wettability of sphalerite (110) surface

The effect of impurities in the zinc sulfide mineral sphalerite on surface wettability has been investigated theoretically to shed light on previously reported conflicting results on sphalerite flotation. The effect of iron and copper impurities on the sphalerite (110) surface energy and on the water adsorption energy was calculated with the semi-empirical method modified symmetrically orthogonalized intermediate neglect of differential overlap (MSINDO) using the cyclic cluster model. The effect of impurities or dopants on surface energies is small but significant. The surface energy increases with increasing surface iron concentration while the opposite effect is reported for increasing copper concentration. The effect on adsorption energies is much more pronounced with water clearly preferring to adsorb on an iron site followed by a zinc site, and copper site least favorable. The theoretical results indicate that a sphalerite (110) surface containing iron is more hydrophilic than the undoped zinc sulfide surface. In agreement with the literature, the surface containing copper (either naturally or by activation) is more hydrophobic than the undoped surface.     

碘和氧修饰银(110)表面对甲醇吸附的影响: 密度 泛函理论的计算研究

用密度泛函理论(DFT)的B3-LYP方法和原子簇模型研究了碘和修饰银(110)表面对甲醇吸附的影响。结果表明,甲醇分子在干净的银表面吸附很弱甚至不吸附,但在氧或碘修饰过的银表面上,由于预吸附导致吸附能的增加而变得容易吸附。并进一步采用目前较新的映像电荷模型计算验证了在甲醇部分氧化制甲醛反应中氧或碘对银催化剂表面修饰的本质是电荷修饰这一推论,为实验中如何筛选修饰提供了良好的判据。     

Pt/Cu(001)-p(2×2)-O表面吸附结构的总能计算

采用密度泛函理论(DFT)研究了氧吸附后Pt/Cu(001)表面合金的原子结构和表面性质. 计算结果表明, 在Pt/Cu(001)-p(2×2)-O表面最稳定结构中, 衬底表面原子层不发生再构, 氧原子吸附于4重对称的Pt原子谷位, 每个氧原子吸附能约为2.303 eV. 吸附结构的Cu—O和Pt—O键键长分别为0.202和0.298 nm, 氧原子的吸附高度ZCu—O约为0.092 nm. 吸附前后Pt/Cu(001)-1ML(monolayer)表面合金的表面功函数分别为4.678和5.355 eV. 吸附表面氧原子和衬底的结合主要来自氧原子2p轨道和衬底金属原子d轨道的杂化作用, 氧原子吸附形成的表面电子态主要位于费米能级以下约-2.7 eV 处.