The Influence of Chemical Change on Protein Dynamics: A Case Study with Pyruvate Formate-Lyase

Pyruvate formate-lyase (PFL) catalyzes the reversible conversion of pyruvate and coenzyme A (CoA) into formate and acetyl-CoA in two half-reactions. For the second half-reaction to take place, the S−H group of CoA must enter the active site of the enzyme to retrieve a protein-bound acetyl group. However, CoA is bound at the protein surface, whereas the active site is buried in the protein interior, some 20–30 Å away. The PFL system was therefore subjected to a series of extensive molecular dynamics simulations (in the μs range) and a host of advanced analysis procedures. Models representing PFL before and after the first half-reaction were used to examine the possible effect of enzyme acetylation. All simulated structures were found to be relatively stable compared to the initial crystal structure. Although the adenine portion of CoA remained predominantly bound at the protein surface, the binding of the S−H group was significantly more labile. A potential entry channel for CoA, which would allow the S−H group to reach the active site, was identified and characterized. The channel was found to be associated with accentuated fluctuations and a higher probability of being in an open state in acetylated systems. This result suggests that the acetylation of the enzyme assumes a prominent functional role, whereby the formation of the acyl intermediate serves to initiate a subtle signaling cascade that influences the protein dynamics and facilitates the entry of the second substrate.     

A quantum chemistry study: a new kind of boron nitrides

At the B3LYP/6-311+G** and the BP86/6-311+G** levels of theory, BNN, H(3)BNN, NNBH(2)-BH(2)NN, (BNN)(2)H(2), NNBBNN, (BNN)(3) (+), (BNN)(4), (BNN)(4) (2+), (BNN)(4) (2-), B(4)(NN)(2), (BNN)(5) (-), (BNN)(6), (BNN)(7) (+), and (BNN)(8) (2+) are investigated. Neutral (BNN)(4) is aromatic with its triplet state but antiaromatic with its singlet state. (BNN)(4) dication favors D(2d) structure, while (BNN)(4) dianion favors a planar D(4h) structure. (BNN)(3) (+), (BNN)(4) (2-), (BNN)(5) (-), (BNN)(6), (BNN)(7) (+), (BNN)(7) (3-), (BNN)(8) (2+), and (BNN)(8) (2-) are all aromatic with planar monocyclic conformation, following the 4n + 2 rule. Moreover, according to the CASSCF and MRCI calculations, the planar B(4)(NN)(2) of D(2h) symmetry prefers to be a sigma-pi diradical in spite of open-shell singlet or triplet and is also aromatic. Akin to the sigma-pi back interaction in compounds containing transition metal, there exists the sigma-pi back interaction between boron and N(2) ligand among some species reported herein, which strengthens B(-)N bond but activates N-N bond, especially in (4)Sigma(-) BNN. The T-shaped structure lies lowest in energy among seven isomers of the (BNN)(2)H(2) dimer, and the parallel-displaced structure is favored between two isomers of the (BNN)(6) dimer.     

CIO自由基与CN自由基反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论（DFT）对CIO与CN的双自由基反应进行了研究．结果表明,CIO自由基的O原子进攻CN自由基的C原子是主要的进攻方式,并形成了中间体1 CIOCN．随后,中间体1发生异构化和分解反应得到热力学上可行的3种产物P4（CINCO）,P1（CO＋CIN）和P3（NO＋CCl）．其中P4是主要产物,P1和P3是次要产物．与单态势能面上相比,三态势能面对整个反应的贡献可以忽略．     

Theoretical investigation of unimolecular decomposition channels of furan4

Density functional theory and high-level ab initio calculations were carried out to investigate three unimolecular decomposition channels of furan. All equilibrium and transition state structures along the proposed decomposition channels are fully optimized by B3LYP/6-31G** and characterized at the same level of theory by vibrational and intrinsic reaction coordinate analyses. Relative energies of the optimized structures were evaluated at theoretical levels up to QCISD(T)/6-311++G**. The theoretical results suggest that the unimolecular decomposition channel of isoxazole, proposed in an experimental study and implied to be the main decomposition channel of furan, is responsible only for the formation of HC(TRIPLE BOND)CH and H₂O(DOUBLE BOND)C(DOUBLE BOND)O, minor products of furan thermal decomposition. A new decomposition mechanism, proposed in the present study, is shown to be more likely responsible for the formation of CH₃C(TRIPLE BOND)CH and CO, major products of furan thermal decomposition. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 240–249, 1998     

The interaction of water with sulfonium ions and the effects of hydration on the energetics of methyl group transfer: An ab initio molecular orbital study of the hydration of (CH3)3S+ and (CH3)2S+CH2CO2 −

The interactions of the sulfonium ions (CH₃)₃S⁺, (CH₃)₂S⁺CH₂CO₂ ^–, and (CH₃)₂S⁺-CH₂CH₂CO₂ ^– with up to four water molecules have been studied by ab initio molecular orbital methods. Complexes of (CH₃)₃S⁺ with one to three water molecules involve strong electrostatic sulfur-oxygen interactions; in contrast, the sulfide (CH₃)₂S interacts with water molecules via weak S-H hydrogen bonds, suggesting that methyl-group transfer from (CH₃)₃S⁺ in aqueous solution involves a significant alteration of the hydration pattern around the sulfur atom. Two conformers of (CH₃)₂S⁺CH₂CO₂ ^– were found that display sulfur-oxygen distances which are approximately 0.3 å less than the sum of the sulfur and oxygen van der Waals radii, indicating a strong intramolecular electrostatic interaction. For the complexes (CH₃)₂S⁺CH₂CO₂ ^–·nH₂O(n =1–4), water interacts primarily with the carboxylate group via hydrogen bonds, rather than electrostatically with the sulfur atom, although in complexes with the three- and four-water complexes, the proximity of the positively charged sulfur atom to the carboxylate group significantly alters the hydration pattern compared to that in the corresponding of complexes CH₃SCH₂CO₂ ^–· Thus, methyl transfer from (CH₃)₂S⁺CH₂CO₂ ^– to an acceptor in aqueous solution also involves substantial changes in the hydration pattern around the carboxylate group.     

CHF_2CF_2CH_2OCHF_2与OH自由基反应机理的理论研究

采用从头算和密度泛函方法研究了多通道反应CHF2CF2CH2OCHF2+OH→产物的反应机理.首先在BMK/6-311+G(d,p)水平下优化了稳定点的几何构型并计算了振动频率;然后在BMC-CCSD水平下,对势能面进行高水平能量校正.结果表明,此反应存在提氢和取代两类反应通道,但是无论从动力学还是从热力学分析,提氢反应通道才是主要的反应通道,且从-CH2-基团上提取氢原子的提氢通道是主要的反应通道.     

Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions

An efficient approach for quantitative modeling of liquid phase photoelectron spectra, reorganization energies, and redox potentials with DFT‐based molecular dynamics simulations is presented. The method is based on a large scale cluster‐continuum approach combined with the so‐called reflection principle (RP). Finite size clusters of solute molecules with solvating water molecules are at first generated using either classical molecular dynamics or molecular dynamics with a quantum thermostat which accounts for nuclear quantum effects. In the next step, the electron binding energies are calculated. Finite‐size corrections for (i) positions of electron binding energies and (ii) width of the spectrum are evaluated via a dielectric continuum approach. The performance of such a reflection principle with additional broadening approach (RP‐AB) for oxidation of multiply charged iron anions, [Fe(CN)₆]⁴⁻ and [Fe(CN)₆]³⁻ is demonstrated. The role of nuclear quantum effects is discussed as well as the relation between spectroscopic data and electrochemical quantities. Results are compared with recent liquid photoemission experiments, explaining the obstacles for applying liquid phase photoemission spectroscopy as a direct method for obtaining absolute redox potentials and suggesting a way to overcome them. © 2017 Wiley Periodicals, Inc.     

氧气和CS自由基反应势能面的密度泛函理论研究

应用量子化学从头计算和密度泛函理论(DFT)对O_2和CS自由基的反应进行了研 究。在B3LYP/6-311G~(**)水平上计算出了各物种的优化构型、振动频率和零点振 动能(ZPVE)。各物种的总能量由CCSD（T）/6-311G~(**)//B3LYP/6-311G~(**)给出 ，并对总能量进行了零点能校正。计算结果表明：CS自由基中的C端沿着O_2的双键 中线方向进攻，进行加成反应，反应的第一步放出大量的热量(450 kJ/mol)，推动 反应继续进行，从稳定的中间体4(Cs)出发，反应主要通过O的相邻位置的迁移生成 P_1(CO+SO)和P_3(COS+O)；通过S的相邻位置的迁移生成了重要的反应复合物 (complex 1)，进一步离解为产物P_2(CO_2+S)。计算结果可以很好地解释反应机理 。     

Computational modeling of strained alkenes: Choosing the right computational model

The applicability of 12 different quantum chemical calculation methods, including density functional theory (DFT) and ab initio methods, for describing strained alkenes and modeling their gas‐phase basicities (GB), hydrogenation enthalpies, and double bond geometries was studied for a series of systematically defined compounds R1R2C = CR3R4. The calculated values were compared to experimental data that had been compiled from literature for several compounds within the series. The closest relationship between the computational results and experimental data occurred with the G2MP2 ab initio method. The best DFT method for GB values was M062X and for hydrogenation enthalpies PBEPBE. At the same time, the relative effects of compound structure variations on the calculated values were similar among all 12 of the calculation methods tested. The double bond length was relatively insensitive to the sizes of the R substituents in R1R2C = CR3R4, but the torsion angles changed significantly in response to structural changes to the compounds when none of the groups R1–R4 was hydrogen.     

Computational study of the reaction of the methylsulfonyl radical,CH3S(O)2, with NO2

The mechanism of the reaction between the methylsulfonyl radical, CH₃S(O)₂, and NO₂ is examined using density functional theory and ab initio calculations. Two stable association intermediates, CH₃SNO₂ and CH₃S(O)ONO, may be formed through the attack of the nitrogen or the oxygen atom of NO₂ radical to the S atom. Interisomerization and decomposition of these intermediates are investigated using high level energy methods and specifically, CCSD(T), CBS‐QB3, and G3//B3LYP. The computational investigation indicates that the lowest energy reaction pathway leads to the products CH₃S(O)₃ + NO, through the decomposition of the most stable association adduct CH₃S(O)ONO. This result fully supports the relevant assumption of Ray et al. (Ray et al., J. Phys. Chem. 1996, 100, 8895], on which the experimental evaluation of the rate constant was based, namely that CH₃S(O)₃ + NO are the most probable products of the reaction CH₃S(O)₂ + NO₂. © 2014 Wiley Periodicals, Inc.     

Intermediate carbene formation in the reaction of thioamides with phosphorus (III) derivatives: Quantum chemical investigation

The reactions of perfluoroalkyl thioamides with trimethyl phosphine, trimethyl phosphite, and tris(dimethylamino)phosphine have been analyzed by means of quantum chemical (DFT and MP2) calculations. The reaction seems to proceed via the nucleophilic attack of the electrophilic carbon atom by the phosphorus lone pair with the formation of cyclic or acyclic adducts. The latter releases the thiophosphate molecule forming perfluoroalkylaminocarbene as the short‐lived intermediate. The reaction of the carbene with the second molecule of trialkyl phosphite yields phosphorus ylide. The ylide undergoes a migration of fluorine from carbon to phosphorus. The reactions of perfluoroalkyl thioamides with phosphines and tris(dimethylamino)phosphine probably proceeds differently. Using alkyl thioamides or amides instead of perfluoroalkyl thioamides also makes the reaction less favorable. The only combination of perfluoroalkyl thioamides with trialkyl phosphite fulfills both the kinetic requirements (moderate activation energies and relative energies for intermediates) and the thermodynamic aspects (higher stabilities of the reaction products compared with the starting materials). © 2013 Wiley Periodicals, Inc.     

Interaction of angelicin with DNA‐bases (III) DFT and ab initio second‐order Moeller–Plesset study

Angelicin geometry was optimized at MP2/6‐31+G(d,p) level and compared with X‐ray experimental data. The highest π‐electron density was found to be localized on C1? C2 and on C13? C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD‐DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc‐pVDZ, MP2/6‐31G(d,p) and MP2/cc‐pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

用从头算研究Shilov反应的机理

Shilov反应在CH~4活化中占有中心地位,它有氧化加成和σ迁移两种可能的机理。本文用较大基组的从头算研究了这两种机理的反应过程,认为Shilov反应应按氧化加成机理进行。     

8-羟基喹啉铝光电性质的Ab initio和DFT研究

利用abinitioHF和密度泛函理论B3LYP等方法,对金属有机配合物8-羟基喹啉铝(AlQ₃)进行几何结构优化,探索分子内部电子跃迁的机理.结果表明,电子从基态跃迁到低激发态时主要为π-π^*跃迁;电荷从含氧的苯酚环转移至含氮的吡啶环上,包括两环之间C→C转移和O→N转移,与金属离子关系不大.考虑到配体对发光性质的贡献,进一步设计了3种AlQ₃的衍生物.     

N,N-Dimethylaminopropylsilane: a case study on the nature of weak intramolecular Si...N interactions

N,N-Dimethylaminopropylsilane H(3)Si(CH(2))(3)NMe(2) was synthesised by the reaction of (MeO)(3)Si(CH(2))(3)NMe(2) with lithium aluminium hydride. Its solid-state structure was determined by X-ray diffraction, which revealed a five-membered ring with an SiN distance of 2.712(2) A. Investigation of the structure by gas-phase electron diffraction (GED), ab initio and density functional calculations and IR spectroscopy revealed that the situation in the gas phase is more complicated, with at least four conformers present in appreciable quantities. Infrared spectra indicated a possible SiN interaction in the Si-H stretching region (2000-2200 cm(-1)), as the approach of the nitrogen atom in the five-membered ring weakens the bond to the hydrogen atom in the trans position. Simulated gas-phase IR spectra generated from ab initio calculations (MP2/TZVPP) exhibited good agreement with the experimental spectrum. A method is proposed by which the fraction of the conformer with a five-membered ring can be determined by a least-squares fit of the calculated to experimental absorption intensities. The abundance of this conformer was determined as 23.7(6) %, in good agreement with the GED value of 24(6) %. The equilibrium SiN distance predicted by theory for the gas-phase structure was highly variable, ranging from 2.73 (MP2) to 3.15 A (HF). The value obtained by GED is 2.91(4) A, which could be confirmed by a scan of the potential-energy surface at the DF-LCCSD[T] level of theory. The nature of the weak dative bond in H(3)Si(CH(2))(3)NMe(2) can be described in terms of attractive inter-electronic correlation forces (dispersion) and is also interpreted in terms of the topology of the electron density.     

DFT Study of the Mechanism and Regioselectivity of 1,3-Pentadiene with Methyl Acrylate Using Theoretical Approaches

<正>Ab initio density functional theory (DFT) calculations have been used to study regioselectivity in the Diels-Alder (DA) cycloaddition reaction between 1,3-pentadiene and methyl acrylate. The DFT calculations were performed with the B3LYP functional and 6-311+G~(**) basis set. Two synchronous transition structures corresponding to the formation of different regioisomers associated with the two reaction channels have been located. The DFT calculations generated transition geometries with a very small degree of asynchronicity. The present analysis shows that these reactions have normal electron demand (NED) character. Moreover, the results obtained from energetic and electronic approaches with the exception of Houk's rule confirm that ortho regioisomer is the major product.     

Structural chemistry of organotin carboxylates: a review of the crystallographic literature

This review describes the structural chemistry of organotin carboxylates, covering data acquired for mono-, di- and tri-organotin compounds and complexes. A brief discussion is given for organotin amino-acid derivatives.     

Interactions of water and methanol with a mixture of copper and zinc metals: a theoretical <Emphasis Type="Italic">ab initio</Emphasis> study

Ab initio cluster quantum chemical calculations at the Hartree–Fock and second-order Møller–Plesset perturbation theory levels were carried out to mimic the interactions of water and methanol with a mixture of Cu and Zn metals. It was shown that both molecular and dissociative adsorption of methanol on a mixture of Cu and Zn metal catalyst are preferred over the corresponding adsorptions of water. Estimated transition-state structures for dissociation of methanol into CH·₃ and OH· lie about 9.0 and 22.0 kcal/mol higher compared to the dissociated (forward reaction) and molecular adsorption (reverse reaction) complexes, respectively. Based on distinct radicals' bond energies with the active sites of the catalyst considered, it is suggested that hydrogen molecules could be formed through a chain of homogeneous reactions of methyl radicals released into the gas phase with the water and/or methanol molecules.