Theoretical studies of sulbactam: Reactions after acylation

DFT methods were used on the model molecular to determine the mechanism of β‐lactamase inhibitor. The results show that the thiazole ring can be opened as well as β‐lactam ring. The thiazole ring‐open product can be formed via β‐lactam ring‐open product or tetrahedral intermediate directly. Those products, in imine or enamine form, can tautomerize via hydrogen migration. The sulforious form products may be transformed into sulfonyl ones. Water or hydroxyl group in residues on active site will help lower the activation energy of above reactions, and if structure permitted, they also effect the route selection of whole reaction system. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Fluorides of ruthenium and chromium: Theoretical studies

The electronic and structural characteristics of CrF₅, CrF₄, RuF₅ and RuF₄ were studied. Ab initio (SCF-CI) calculations were performed with different structures and spin states for each complex. The favored conformation always corresponds to the highest multiplicity: doublet for CrF₅ in D_3h, triplet for CrF₄ in T_d, quadruplet for RuF₅ in C_4v and quintuplet for RuF₄ in D_4h symmetry.     

Theoretical studies in molecular recognition: Rebek's cleft

Molecular recognition in Rebek's cleft was studied with the MM2 force field. A new computational protocol was used to determine the free energies of substrate binding to this topologically unique model receptor. The energies and structural features of substrate-receptor complexes reveal that molecular recognition involves ammonium ion binding to the interior of the cleft and aromatic π-stacking on the exterior of the cleft.     

Theoretical studies of azapentalenes. Part 5: Bimanes

The properties of 21 molecules related to azapentalenes and their conjugated acids have been calculated: energies, dipole moments, natural bond orders, bond lengths, bond critical points, HOMA, and NICS. The ring-opening processes of dioxopyrazolo[1,2-a] pyrazolium and pyrazolo[1,2-a][1,2,4]triazol-4-ium into ketenes and isocyanates have been studied. The calculations were carried out at the B3LYP/6-311++G(d,p) level.     

Electronic structure and bonding in clusters: Theoretical studies

The electronic structures of small Al _n ,n=5, 9, 13, clusters with bulk geometry are studied using the ab initio Hartree-Fock-LCAO method. The cluster ground states have always multiplicity higher than the lowest possible value. However, the energy difference between ground and lowest low spin state decreases with increasing cluster size. The energy range of the Al _n cluster valence levels is comparable with the width of the occupied part of the 3sp band in bulk Al. The different binding mechanisms that arise when a CO molecule interacts with Al _n clusters in different coordination sites are analyzed in detail with the constrained space orbital variation (CSOV) method. Electrostatic and polarization contributions to the interaction are found to be important. Among charge transfer (donation) contributions π electron transfer from Al _n to CO corresponding to π backbonding is energetically more important than σ electron transfer from CO to Al _n characterizing the σ bond.     

Theoretical studies on hydroquinone-benzene clusters

High-level ab initio calculations were carried out to evaluate the interaction between the hydroquinone and benzene molecules. The intermolecular interaction energy was calculated using the M?ller-Plesset second-order perturbation theory at the complete basis set limit and also at the coupled cluster theory with single, double, and perturbatively triple excitations. The calculated binding energy is larger than the benzene dimer interaction energy. The T-shaped cluster (T-a) and the parallel conformation (P-a) are calculated to be nearly isoenergetic. Owing to the large energy gain in the attraction by electron correlation, the dispersion interaction is important for the attraction.     

Theoretical studies of stereoselective hydroborations

Asymmetric hydroborations of alkenes are outstanding examples of reactions which proceed with high acyclic stereoselection to give synthetically useful functionality. We have undertaken com- putational studies of these reactions as a part of our more general studies of stereoselective organic reactions. We wish to develop understanding of those factors which control stereoselectivity in known cases, and to develop both qualitative and quantitative methods to predict stereoselectivities of cases not yet investigated. Here, we detail our progress in understanding hydroborations, and in subsequent publications, we will report similar studies for other types of organic reactions, such as intermolecular and intramolecular cycloadditions, epoxidations, radical reactions, nucleophilic additions, and aldol condensations.     

Theoretical studies of ion neutralization: Two-dimensional tight binding models

The neutralization of ions impinging on a substrate is modeled by treating the substrate as both a two-dimensional, tight-binding, semi-infinite sheet and a two-dimensional, tight-binding, infinite sheet. In both cases the equations of motion are set up in a generalized Langevin format. Results are presented for a model interaction and compared with previous computations using a semi-infinite chain model and an infinite chain model.     

Theoretical studies on farnesyl cation cyclization: pathways to pentalenene

In this article, we describe studies, using quantum chemical computations, on possible polycyclization pathways of the farnesyl cation leading to the complex sesquiterpene pentalenene. Two distinct pathways to pentalenene with similar activation barriers are described, each differing from previous mechanistic proposals, and each involving unusual and unexpected intermediates. Direct deprotonation of intermediates on these pathways leads to sesquiterpene byproducts, such as humulene, protoilludene, and asteriscadiene, supporting the notion that a key function of pentalenene synthase, the enzyme that produces pentalenene in Nature, is to regulate the timing and location of proton removal. The implications of the computational results for experimental studies on pentalenene synthase are discussed.     

Theoretical studies on titanium pentafulvene complexes

A series of six titanium pentafulvene complexes are thoroughly investigated using the B3LYP/6-31G(d) level of theory. Excellent agreement with the available structural data is obtained. Relevant structural parameters indicate that a gradual change of the fulvene ligand coordination to the titanium center. Depending on the nature of the exocyclic fulvene substituents dianionic η⁵, η¹-and olefinic η⁶-coordination modes are found. This behavior is further supported by NBO and AIM population analyses which predict differences in the bond nature meanly of the contacts between titanium and the exocyclic carbon atom. In an excitation study, several theoretical approaches are evaluated against the available recorded UV-Vis spectra of the six complexes. The “best” approach, time-dependant DFT calculations reproduce the experimental UV data reasonably well, although systematically slightly too small values (abut 50 cm⁻¹) are obtained. The other levels of theory are significantly more erratic. It could further be testified that the absorption maxima correspond to a ligand-to-metal charge transfer from the HOMO to the LUMO+1 of the complexes.     

Theoretical studies on electrochemistry of p-aminophenol

Geometric parameters, vibrational frequencies and thermochemical values of p-quinonimine (p-Q) and p-aminophenol (p-AP) were computed by ab initio calculation (HF) and density function theory (DFT) with the 6-31G(d,p) basis set. Cyclic voltammetry with a goldren electrode of p-AP solutions in phosphate buffers at pH 7.30 showed that standard electrode potential of half reaction for (p-Q) and (p-AP) is 0.728V. Standard electrode potential of half reaction for p-Q and p-AP were calculated using the sum of electronic and thermal free energies of p-Q and p-AP with normal hydrogen electrode (NHE) as a reference electrode. The results show that the theoretical standard electrode potential of half reaction for p-Q and p-AP is 0.682V at B3LYP/6-31G(d,p) level and 0.622V at HF/6-31G(d,p) level, respectively, indicating that computed standard electrode potential at B3LYP/6-31G(d,p) level are more reliable than that at HF/6-31G(d,p) level.     

二甲基精氨酸二甲胺水解酶-1的理论研究

运用分子对接和分子动力学方法研究二甲基精氨酸二甲胺水解酶-1(DDAH-1)与其抑制剂亚胺基烯丁基-L-鸟氨酸(L-VNIO)和亚胺基丙基-L-鸟氨酸(Me-L-NIO)的相互作用和结合模式,并根据实验得到的结论设计了亚胺基苯乙基-L-鸟氨酸(Ph-L-NIO)抑制剂.结果表明:L-VNIO比Me-L-NIO对DDAH-1的抑制效果更强,这个结果与实验测得L-VNIO和Me-L-NIO对DDAH-1的半抑制浓度IC50值大小一致.Phe75、Asp78、His172、Ser175和Asp268这五个氨基酸残基在三种抑制剂形成的复合物中起到非常重要的作用,从计算结果推断在这三个抑制剂中我们设计得到的Ph-L-NIO对DDAH-1的抑制效果最好.     

Theoretical studies of borazynes and azaborines

Four isomers of didehydroborazine, B3N3H4, borazyne, and three isomers of azaborine, C4H4BN, are studied by DFT, CCSD, and CCSD(T) computational methods. The singlets of 1,2-borazyne (I) and 1,4-borazyne (IV) have angles about the boron of ca. 150 degrees . In 1,2-azaborine (V), the angles are ca. 140 degrees , while the N angles are ca. 112 degrees except in IV (127 degrees ) and 1,4- azaborine (VII, 120 degrees ). These geometries are almost reversed in the triplets. The 1,3-borazyne (III) shows more bicyclic character than the corresponding m-benzyne, with an N-N distance of 1.7 A. In all cases I was found to be lower in energy than the 2,4-borazyne (II), III, and IV. The order of stability of the azaborines is V > VII > 1,3- azaborine (VI). The nucleus-independent chemical shift (NICS) indicates that all isomers of borazyne are less aromatic than benzene and all isomers of azaborine are about as aromatic as benzene. Time-dependent DFT (TD-DFT) is used to study the excited states of the singlets. The significant structural differences between the singlet and triplet states suggest long phosphoresence lifetimes.     

Theoretical studies of the inductive effect

Ab-initio calculations (STO-3G) show no evidence for σ-inductive effects in the dissociation of certain alkylammonium ions. Substituents effects are suggested to arise from non-bonded interactions and polarisation of CH bonds as well as from direct field effects.     

Theoretical studies of microfluidic dispensing processes

The understanding of electrokinetic transport phenomena in microfluidic dispensers, an important component of biochips, is very important for designing and controlling biochips. A theoretical model to study the electrokinetic transport processes in microfluidic dispensers was developed in the work to study the controlling parameters for the dispensing process. The electrical field, the flow field, and the concentration field during dispensing processes were obtained by solving this theoretical model numerically. The effects of the electroosmotic mobility of the buffer solution, the diffusion coefficient and the electrophoretic mobility of the sample, the applied electrical field strength, and the channel size on the dispensing process are examined in this paper. The investigations show that optimal controlling parameter values can be found by using this model for dispensing any desired amount of the sample.     

Hybrid density-functional theory studies on stable polycarbenes

Stable carbene:bis(9-(10-phenyl)anthryl)carbene and model carbenes of which have been investigated by ab initio MO and Crystal orbital calculations. By hybrid density-functional calculation (B3LYP/4-31G) the carbene has character as a triplet carbene than a triplet diradical. Based on calculations on this carbene, a polycarbene is contrived to investigate interactions of carbenes, which are stabilized by aromatic rings. They have interacted with each other in antiferromagnetic fashion by both B3LYP MO and Crystal orbital calculations. Their magnetic interactions have been varied as the conformational changes of the aromatic rings, which have been evaluated by the effective exchange integral J(AP) based on the Heisenberg Hamiltonian. To describe the behavior AO-approach has been introduced and has worked efficiently.     

Theoretical studies of furoxan-based energetic nitrogen-rich compounds

Density functional theory calculations were performed to study the effects of different substituents and nitrogen-containing heterocyclic rings on the heats of formation (HOFs), energetic properties, and thermal stability for a series of furoxan derivatives. The isodesmic reaction method was employed to calculate the HOFs of the derivatives using total energies obtained from electronic structure calculations. The detonation velocities and pressures were evaluated by using the semiempirical Kamlet–Jacobs equations, based on the theoretical densities and HOFs. The bond dissociation energies and bond orders for the weakest bonds were analyzed to investigate the thermal stability of the furoxan derivatives. These results provide basic information for the molecular design of novel high energy density materials.     

Theoretical studies on the formation of N-nitrosodimethylamine

The mechanisms of the formation of N-nitrosodimethylamine (NDMA) were studied at the MP2/6-311+G(d,p)//B3LYP/6-311+G(d,p) level of theory. We focused on the formation of NDMA from the reactions of dimethylamine (DMA) with nitrous acid and nitrite anion. Our calculations show that the reaction of DMA with nitrous acid is predicted to proceed via two distinct pathways: a concerted or a stepwise mechanism. Moreover, the energy barrier for the stepwise mechanism is somewhat higher than that for the concerted mechanism. The difference in these barriers indicates that the reaction of DMA with nitrous acid via the concerted mechanism is much more favored than that via the stepwise mechanism. In the other situation, our results demonstrate that the reaction of DMA with nitrite anion becomes feasible in the presence of carbon dioxide. Furthermore, this reaction proceeds via a stepwise pathway, in which CO₂ first attacks DMA, the result of which then reacts with nitrite anion. It is noteworthy that carbon dioxide appears to be an active catalyst to promote the formation of NDMA. Additionally, the effects of aqueous solvation on the reactions of DMA with nitrous acid and nitrite anion were investigated.