Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O−H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.     

A Computational Study of Conformers of 2-Thiaoxacyclohexane (1,2-Oxathiane)

Ab initio molecular orbital theory with the 6-31G(d), 6-31G(2d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), and 6-311G(d,p) basis sets and the hybrid density functionals B3LYP, B3P86, and B3PW91 have been used to calculate the optimized geometries and relative energies of the chair, half-chair, sofa, twist, and boat structures of 2-thiaoxacyclohexane (1,2-oxathiane). The values of the energy difference (E, kcal/mol) between the chair and 3,6-twist structures of 1,2-oxathiane were 4.92 (HF), 4.73 (MP2), and 4.66 (DFT). The HF chair–twist energy difference (G _c–t ^o) for 1,2-oxathane was 5.16 kcal/mol. Intrinsic reaction coordinate (IRC) calculations connected a transition state (TS-A) between the chair conformation and the less stable 2,5-twist form and connected two transition states (TS-B, TS-C) between the chair conformation and the more stable 3,6-twist conformer. The DFT energy differences between the chair and TS-A, TS-B, and TS-C were 11.4, 10.8, and 12.6 kcal/mol, respectively. Hyperconjugative stereoelectronic interactions were observed in the chair (n _o and ) and 3,6-twist (n _S and n _O ) conformers of 1,2-oxathiane. The chair conformation of 1,2-oxthiane is 9.6 and 10.0 kcal/mol, respectively, less stable than the chair conformations of 3-thiaoxacyclohexane (1,3-oxathiane) and 4-thiaoxacyclohexane (1,4-oxathiane, thioxane).     

Understanding the Regioselectivity and the Molecular Mechanism of [3 + 2] Cycloaddition Reactions between Nitrous Oxide and Conjugated Nitroalkenes: A DFT Computational Study

Regiochemical aspects and the molecular mechanism of the [3 + 2] cycloaddition between nitrous oxide and conjugated nitroalkenes were evaluated on the basis of the wb97xd/6-311 + G(d) (PCM) computational study. It was found that, independently of the nature of the nitroalkene, all considered processes are realized via polar, single-step mechanisms. All attempts at the localization of hypothetical zwitterionic intermediates were unsuccessful. Additionally, the DFT computational study suggested that, in the course of the reaction, the formation of respective Δ²-4-nitro-4-R₁-5-R₂-1-oxa-2,3-diazolines was preferred from the kinetic point of view.     

A Computational Study of the Wallach Rearrangement

Treatment of azoxybenzene and its derivatives with acids is known to result in the Wallach rearrangement, which leads to 2- or4-hydroxyazobenzenes. Starting in the 1960s, experimental findings have lead to the proposal of several mechanisms for this rearrangement. In this work, molecular orbital theory employing the semiempirical AM1 method is used to locate and discuss the energetics of the intermediates and the transition states for this rearrangement. Based on the results of AM1 calculations in vacuum and in solution, the most plausible mechanistic pathways are proposed and discussed.     

氢卟啉和镁卟啉分子溶剂效应的理论研究

采用溶剂场极化连续模型在密度泛函B3LYP/6-31G (D)水平上研究了氢卟啉和镁卟啉分子在四氢呋喃(THF)、二甲基亚砜(DMSO)、二氯甲烷(CH2Cl2)、氯仿(CHCl3)这四种不同极性的溶剂环境中的几何结构和分子轨道能级, 从而研究了溶剂效应引起的分子几何构型和轨道能级的变化. 然后采用上述溶剂环境下优化的几何结构在含时密度泛函水平上计算了它们的激发能、吸收波长、跃迁组成和振荡强度. 理论计算结果表明, 对比真空条件下的氢卟啉和镁卟啉分子的几何结构, 溶剂场中两种卟啉分子的几何结构都发生了微弱的变化, 这种变化随溶剂介电常数的增大而有所增强. 计算结果表明溶剂环境中氢卟啉和镁卟啉分子的电子吸收光谱发生了普遍的红移, 结合分子轨道理论对这种变化给出了可能的解释. 在此基础上, 对这种包含溶剂效应的理论分析方法用于检验卟啉类化合物作为染料敏化太阳能电池光敏剂的可行性作了进一步的探讨.     

The influence of hydrophobic amino acid side groups on the acidity of the aromatic imidazole ring of histidine: A theoretical study

In this study we have calculated the acidity constant (pKa) of imidazole ring in Histidine‐Hydrophobic amino acid dipeptides using the quantum chemistry and continuum solvation methods. Density functional theory calculations with the large basis sets are used to determine the Gibbs free energy of deprotonate in the gas and liquid phases. Based on our results ΔG_S values are located between ?69.38 and ?18.82 kcal mol^?1 which are related to His⁺–Gly and His forms, respectively. pKa of the dipeptides in the aqueous phase was obtained from the calculated gas‐phase and solvation free energies through a thermodynamic cycle and the solvation model chemistry of Martin Karplus et al. Solvation effects are treated using a self‐consistent reaction field formalism involving polarized continuum models. According to our calculations pKa values are between 5.50 and 8.19 that are belong to His⁺–ILe and His⁺–Ala forms, respectively. Natural bond orbital analysis of dipeptides reveals that the electron delocalization in imidazole ring is the most effective factor in determination of acidity order for these compounds. Structural analysis confirmed that the orientation of carbonyl group with respect to imidazole ring is an effective factor in imidazole ring stability. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Conformational Distributions of N‐Acetyl‐L‐cysteine in Aqueous Solutions: A Combined Implicit and Explicit Solvation Treatment of VA and VCD Spectra

The conformational distributions of N‐acetyl‐L ‐cysteine (NALC) in aqueous solutions at several representative pH values are investigated using vibrational absorption (VA), UV/Vis, and vibrational circular dichroism (VCD) spectroscopy, together with DFT and molecular dynamics (MD) simulations. The experimental VA and UV/Vis spectra of NALC in water are obtained under strongly acid, neutral, and strongly basic conditions, as well as the VCD spectrum at pH 7 in D₂O. Extensive searches are carried out to locate the most stable conformers of the protonated, neutral, deprotonated, and doubly deprotonated NALC species at the B3LYP/6‐311++G(d,p) level. The inclusion of the polarizable continuum model (PCM) modifies the geometries and the relative stabilities of the conformers noticeably. The simulated PCM VA spectra show significantly better agreement with the experimental data than the gas‐phase ones, thus allowing assignment of the conformational distributions and dominant species under each experimental condition. To further properly account for the discrepancies noted between the experimental and simulated VCD spectra, PCM and the explicit solvent model are utilized. MD simulations are used to aid the modelling of the NALC–(water)_N clusters. The geometry optimization, harmonic frequency calculations, and VA and VCD intensities are computed for the NALC–(water)_3,4 clusters at the B3LYP/6‐311++G(d,p) level without and with the PCM. The inclusion of both explicit and implicit solvation models at the same time provides a decisively better agreement between theory and experiment and therefore conclusive information about the conformational distributions of NALC in water and hydrogen‐bonding interactions between NALC and water molecules.     

Theoretical Study on the Electronic Structures and Spectral Properties of 1,8-Naphthalimide Derivatives

The molecular geometries, frontier molecular orbital properties, and absorption and emission properties of three 4-phenoxy-1,8-naphthalimide derivatives, namely 4-phenoxy-N-（2-hydroxyethyl）-1,8-naphthalimide（1）,4-（2-tert-butylphenoxy）-N-（2-hydroxyethyl）-1,8-naphthalimide（2）, and 4-[2,4-di（tert-butyl）]phenoxy-N-（2-hydroxyethyl）-1,8-naphthalimide（3）, are investigated by density functional theory（DFT） and time-dependent density functional theory（TD-DFT） calculations in conjunction with polarizable continuum models（PCMs）. Four functionals and ten basis sets are employed for 1 to calculate the electron transition energies, which were compared with the experimental observations. Our results reveal that the B3LYP/6-311＋G（d,p） method is the best choice to reproduce the experimental spectra. Moreover, the effects of substituents on the molecular geometries, electronic structures, absorption and emission spectra are also studied at the B3LYP/6-311＋G（d,p） level. We find that the gap between the highest occupied molecular orbital（HOMO） and the lowest unoccupied molecular orbital（LUMO） decreases with increasing the number of tert-butyl substituents onto the phenoxy groups, suggesting red-shift of the absorption and emission bands. This is related to the increase of conjugation from 1 to 2 and 3. Our calculations are in good agreement with the experimental results.     

Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads

Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain stacked base tetrads with intercalated metal ions as basic building blocks. Thus far, quantum-chemical studies have been used to explore the geometric and energetic properties of base tetrads with and without metal ions. Recently, for the first time, work on a sandwiched G-tetrad complex has been studied. We report here results of a systematic B3LYP density functional study on sandwiched G-, C-, U-, and T-tetrads with Na+ and K+ at different symmetries that substantially extend the recent work. The results include detailed information on total energies as well as on metal ion tetrad and base-base interaction energies. The geometrical parameters of the sandwiched metal ion complexes are compared to both experimental structures and to calculated geometries of complexes of single tetrads with metal ions. A microsolvation model explains the ion selectivity preference of K+ over Na+ in a qualitative sense.     

Structural and Dynamic Properties of Monoclonal Antibodies Immobilized on CNTs: A Computational Study

Due to the widespread application of carbon nanotube (CNT)‐based materials in nanomedicine, it is nowadays of paramount importance to unravel at the atomistic level of detail the structural properties of such bioconjugates in order to rationalize and predict the effect exerted by the graphitic framework on the bio‐active counterpart. In this paper, we report for the first time all‐atom explicit solvent molecular dynamics (MD) simulations investigating the structural and dynamic properties of a noncovalent bioconjugate in which the monoclonal Cetuximab antibody (Ctx) is adsorbed on a CNT surface. Upon selection of the three most representative adsorption modes as obtained by docking studies, force‐field MD and DFT simulations unambiguously showed that hydrophobic interactions mainly govern the adsorption of the protein on the graphitic surface. Two main adsorption poses have been predicted: a pose‐fab (p‐fab) and pose‐fc (p‐fc) (fab = fragment antigen binding region; fc = fragment crystallizable region), the former being favored with small‐diameter tubes (≤40 Å). In all the predicted poses, the secondary structure of Ctx is largely unaffected by the presence of the graphitic surface and, consistently with previous literature studies, our simulations reveal that positively charged amino acidic residues, such as Lys and Arg, predominantly contribute to the stabilization of the CNT?Ctx complex acting like surfactants. The predicted structural models are consistent with the experimental data, for which the immobilization of the antibody on CNTs does not disrupt the structural and recognition properties of the Ctx, consequently supporting the reliability of the used bioconjugation strategy for engineering stable and responsive hybrid nanomaterials for therapeutic applications. Moreover, a remarkable structural similarity of Ctx with antibodies of different isotypes suggests that in principle the CNT framework can interact in the same manner with all antibodies currently used in clinical applications.     

A Theoretical Study on the Inclusion Complexation of Cyclodextrins with Inorganic Cations and Anions

PM3 and B3LYP/3-21+g(d) calculations were performed on theinclusion complexation of- and -cyclodextrin with inorganic cationsand anions includingLi⁺, Na⁺, F^-, and Cl^-. Both the gas-phase interaction and solvent effect weretaken into consideration. The CD complex with an anionwas more stable than that with acation, which was in agreement with the experimentalfindings. It was proposed thathydrogen bonding between the anion and the cyclodextrincavity was the physical origin ofsuch behavior.     

Structure of 4-[4-(Dimethylamino)-Phenylazo] Benzeneboronic Acid and Its Cyclic Esters with D-Glucose: A Computational Study

We present results from a computational study of 4-[4-(dimethylamino)-phenylazo] benzene boronic acid (DABBA) (the 4'-boronic acid isomer of the aminoazobenzene dye N,N-dimethylaminoazobenzene) and its associated anion, as well as, several cyclic esters formed from these azoborates and various conformers of D-glucose. Azo dyes that also contain one or more boronic acid functional groups are of practical importance in the development of chemical sensors for saccharide recognition because of their ability to induce a visible color change upon binding. The lowest-energy DABBA:D-glucose esters found in this investigation consistently involved at least one of the exocyclic hydroxymethyl groups on the D-glucose moiety rather than vicinal cis or trans diol arrangements of hydroxyl groups on the ring.     

Phosphorene Supported Single-Atom Catalysts for CO Oxidation: A Computational Study

Single-atom catalysts (SACs) have attracted extensive attention owing to their high catalytic activity. The development of efficient SACs is crucial for applications in heterogeneous catalysis. In this article, the geometric configuration, electronic structure, stabilitiy and catalytic performance of phosphorene (Pn) supported single metal atoms (M=Ru, Rh, Pd, Ir, Pt, and Au) have been systematically investigated using density functional theory calculations and ab initio molecular dynamics simulations. The single atoms are found to occupy the hollow site of phosphorene. Among the catalysts studied, Ru-decorated phosphorene is determined to be a potential catalyst by evaluating adsorption energies of gaseous molecules. Various mechanisms including the Eley-Rideal (ER), Langmuir-Hinshelwood (LH) and trimolecular Eley-Rideal (TER) mechanisms are considered to validate the most favourable reaction pathway. Our results reveal that Ru−Pn exhibits outstanding catalytic activity toward CO oxidation reaction via TER mechanism with the corresponding rate-determining energy barrier of 0.44 eV, making it a very promising SAC for CO oxidation under mild conditions. Overall, this work may provide a new avenue for the design and fabrication of two-dimensional materials supported SACs for low-temperature CO oxidation.     

Effect of the Solute Cavity on the Solvation Energy and its Derivatives within the Framework of the Gaussian Charge Scheme

The treatment of the solvation charges using Gaussian functions in the polarizable continuum model results in a smooth potential energy surface. These charges are placed on top of the surface of the solute cavity. In this article, we study the effect of the solute cavity (van der Waals-type or solvent-excluded surface-type) using the Gaussian charge scheme within the framework of the conductor-like polarizable continuum model on (a) the accuracy and computational cost of the self-consistent field (SCF) energy and its gradient and on (b) the calculation of free energies of solvation. For that purpose, we have considered a large set of systems ranging from few atoms to more than 200 atoms in different solvents. Our results at the DFT level using the B3LYP functional and the def2-TZVP basis set show that the choice of the solute cavity does neither affect the accuracy nor the cost of calculations for small systems (< 100 atoms). For larger systems, the use of a vdW-type cavity is recommended, as it prevents small oscillations in the gradient (present when using a SES-type cavity), which affect the convergence of the SCF energy gradient. Regarding the free energies of solvation, we consider a solvent-dependent probe sphere to construct the solvent-accessible surface area required to calculate the nonelectrostatic contribution to the free energy of solvation. For this part, our results for a large set of organic molecules in different solvents agree with available experimental data with an accuracy lower than 1 kcal/mol for both polar and nonpolar solvents.     

Probing Rapidly‐Ionizing Super‐Atom Molecular Orbitals in C60: A Computational and Femtosecond Photoelectron Spectroscopy Study

Super‐atom molecular orbitals (SAMOs) are diffuse hydrogen‐like orbitals defined by the shallow potential at the centre of hollow molecules such as fullerenes. The SAMO excited states differ from the Rydberg states by the significant electronic density present inside the carbon cage. We provide a detailed computational study of SAMO and Rydberg states and an experimental characterization of SAMO excited electronic states for gas‐phase C₆₀ molecules by photoelectron spectroscopy. A large band of 500 excited states was computed using time‐dependent density functional theory. We show that due to their diffuse character, the photoionization widths of the SAMO and Rydberg states are orders of magnitude larger than those of the isoenergetic non‐SAMO excited states. Moreover, in the range of kinetic energies experimentally measured, only the SAMO states photoionize significantly on the timescale of the femtosecond laser experiments. Single photon ionization of the SAMO states dominates the photoelectron spectrum for relatively low laser intensities. The computed photoelectron spectra and photoelectron angular distributions are in good agreement with the experimental results.     

Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study

Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.     

Development of a new density functional program for all-electron calculation of proteins

In this article, we propose a new molecular orbital program for all-electron calculation of proteins which is based on density functional theory. To carry it out in a fully analytical way, we adopted the (pure-) analytical Xα method and modified it for saving a lot of memories for large-scale calculations. The recent software technology sophisticated in information science is inevitably applied to achieve calculations of large molecular systems. The program is coded by the object-oriented language C + +, its output is shown graphically, and the most of the procedures in this program are controlled through an efficient graphical user interface developed by ourselves. Such technology supports the safe construction of the huge software, the tidy representation of enormous data, and the ready control of complex calculations. Test calculations with various sizes of glycine polypeptides indicate that the computation time is proportional to the 1.7 powers of the number of residues. This result suggests that the all-electron calculations of proteins consisting of over 1000 atoms could be performed with distributed and/or massively parallel computers. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63: 245–256, 1997     

Reaction mechanisms of methanol oxidation by FeIVO biomimetic complex

Density functional theory calculations were carried out to investigate the reaction mechanism of methanol oxidation mediated by [(bpg)Fe^IVO]⁺ ( A ). Two models (CH₃CN‐bound ferryl model B and CH₃OH‐bound ferryl model C ) were also studied in this work to probe ligand effect. Mechanistically, both direct and concerted hydrogen transfer (DHT and CHT) pathways were explored. It is found that the initial step of methanol oxidation by A is C? H bond activation via a DHT pathway. Addition of different equatorial ligands has considerable influence on the reaction mechanisms. Methanol oxidation mediated by B commences via O? H bond activation; in sharp contrast, the oxidation mediated by C stems from C? H bond activation. Frontier molecular orbital analysis showed that the initial C? H bond activation by all these model complexes follows a hydrogen atom transfer (HAT) mechanism, whereas O? H bond activation proceeds via an HAT or proton transfer. © 2016 Wiley Periodicals, Inc.     

A radial probability density function for analysis of canonical molecular orbitals

A one‐dimensional probability density function, analogous to the atomic radial density for the hydrogen atom, r²R_nl(r), is defined for an arbitrary three‐dimensional density. It is obtained numerically by taking the derivative of a cumulative probability distribution with respect to the cubic root of the volume enclosed by each in a series of isosurfaces. Each point in the function is associated with a unique isosurface, and the isosurface associated with the maximum of the defined function represents the most probable isosurface with respect to the putative radius. This function therefore provides an objective selection criterion for a single isosurface to represent a three‐dimensional density. This technique is applied to set of canonical molecular orbitals. The selected threshold value varies from orbital to orbital, but the enclosed probability falls in the range of 20% to 55% for the reported orbitals. In all cases, the enclosed probability is much smaller than the common choices found in the literature. The concomitant smaller volume often makes possible a more localized interpretation and helps to clarify the conventional delocalized interpretation of molecular orbitals. For example, the isosurface plots selected by this method distinguish the formally bonding orbital in He₂ from the true bonding orbital in H₂. Examples from N₂, F₂, HF, H₂O, C₂H₆, and Ni(CO)₄ are also presented. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 310–321, 2000     

Electronic Properties of Armchair Graphene Nanoribbons with Oxygen-terminated Edges: A Density Functional Study

Armchair graphene nanoribbons with different proportions of edge oxygen atoms are analyzed in this study using the crystal orbital method,which is based on density functional theory.Although buckled edges are present,all the nanoribbons are energetically favorable.Unlike the adjacent edge oxygen atoms,the isolated edge oxygen atoms cause semiconductor-metal transitions by introducing edge states.For graphene nanoribbons with all oxygen atoms on the edges,band gap and carrier mobility vary with ribbon width.Furthermore,this behavior is different from that of hydrogen-passivated graphene nanoribbons because of different effective widths,which are pictorially presented with crystal orbitals.The carrier mobilities are as 18%~65% magnitude as those of hydrogen-passivated nanoribbons and are of the order of 103 cm2·V-1·s-1.