GPU引发的计算化学革命

综述了图形处理器(GPU)在计算化学中的应用和进展.首先简单介绍了GPU在科学计算中应用的发展,然后分别详细讲述了迄今几个使用GPU和CUDA(compute unified device architecture,显卡厂商Nvidia推出的计算平台)开发工具设计的量子化学计算和分子动力学(MD)模拟的算法和程序,尤其对目前唯一完全使用GPU技术开发的量子化学计算软件TeraChem做了完备的介绍,包括算法、实现的细节和程序目前的功能.此外,本文还对GPU在计算化学上将会发挥的作用做出了极为乐观的展望.     

北京宏剑讯科软件技术有限公司常用化学软件

Gaussian0 3———业界应用最广泛的量子化学软件 ,是作半经验计算和从头计算使用最广泛的量子化学软件。可以研究 :分子能量和结构 ,过渡态的能量和结构化学键以及反应能量 ,分子轨道 ,偶极矩和多极矩 ,原子电荷和电势 ,振动频率 ,红外和拉曼光谱 ,NMR ,极化率和超极化率 ,热力学性质 ,反应路径。计算可以模拟在气相和溶液中的体系 ,模拟基态和激发态 ,还可以对周期边界体系进行计算。公司每月一期G0 3软件培训ADF———化学家的通用密度泛函程序 ,专门作密度泛函计算的软件。ADF基于密度泛函理论 (DFT) ,主要应用于量子化学计算。广…     

ZSM-5分子筛氮化的密度泛函理论研究

利用量子化学中的密度泛函理论,基于ZSM-5分子筛的8T簇模型,在Gaussian 98程序中采用B3LYP方法和6-311G(d,p)基组计算了ZSM-5分子筛中氮的最佳取代位置.计算结果表明,分子筛骨架中氧原子被氮原子取代的最佳位置为O11和O21位.由于位于B酸位上的O11原子是氮原子的最佳取代位置之一,所以氮化可以减弱分子筛表面的B酸强度.     

基于图形处理单元与密度拟合近似的单精度耦合簇CCSD和CCSD(T)程序

作者此前工作表明, 在耦合簇CCSD (Coupled-Cluster approaches within the singles and doubles approximation)与CCSD(T) (CCSD approaches augmented by a perturbative treatment of triple excitations)计算中结合单精度数与消费型图形处理单元(GPU), 可以显著提高计算速度. 然而由于CCSD(T)计算对内存的巨大需求以及消费型GPU的内存限制, 在利用消费型GPU进行加速时, 不考虑利用空间对称性的情况下, 此前开发的CCSD(T)程序仅能用于计算300~400个基函数的体系. 利用密度拟合(Density-Fitting, DF)处理双电子积分可以显著降低CCSD(T)计算过程中的内存需求, 本工作发展了基于密度拟合近似并结合单精度数进行运算的DF-CCSD(T)程序, 该程序可用于包含700个基函数的无对称性体系的单点能计算, 以及包含1700个基函数的有对称性体系. 本工作所使用的计算节点配置了型号为Intel I9-10900k的CPU和型号为RTX3090的GPU, 与用双精度数在CPU上的计算相比, 利用单精度数结合GPU进行运算可以将CCSD的计算速度提升16倍, (T)部分可提升40倍左右, 而使用单精度数引入的误差可忽略不计. 在程序开发过程中, 作者发展了一套可利用GPU或CPU结合单精度数或双精度数进行含空间对称性的矩阵操作代码库. 基于该套代码库, 可以显著降低开发含空间对称性的耦合簇代码的难度.     

镧系元素+3价离子颜色对称性规律的理论研究

本文根据德布罗意关系式和洪特规则,分析了镧系元素+3价离子能量与波长之间的关系,从理论上初步论证和解释了镧系元素+3价离子颜色以钆为中心具有对称性的规律。采用量子化学计算软件——密度泛函理论计算程序ADF,对镧系离子 4f轨道和 5d轨道的能级差进行计算,验证了推论的正确性。     

非平衡溶剂化新理论在有机染料电子光谱中的应用

总结了非平衡溶剂化新理论和在量子化学软件Q-Chem中基于含时密度泛函理论(TD-DFT)实现溶剂效应下计算电子吸收和发射光谱的数值解方法.采用该方法计算了染料敏化太阳能电池(DSSCs)中三苯胺型有机染料■在真空和乙腈溶剂中的电子结构与光谱性质,研究发现,π共轭桥上碳碳双键的个数和溶剂效应会促进光电转换.     

基于平均影响值的反向传播神经网络方法用于提高密度泛函理论计算Y—NO键均裂能精度

将基于平均影响值(Mean impact value,MIV)的反向传播神经网络(Back propagation neural netowrk,BPNN)(MIV-BPNN)方法用于提高密度泛函理论(Density functional theory,DFT)计算Y—NO(Y=N,S,O及C)键均裂能的精度.利用量子化学计算和MIV-BPNN联合方法计算92个含Y—NO键的有机分子体系的均裂能.结果表明,相对于单一的密度泛函理论B3LYP/6-31G(d)方法,利用全参数下的BPNN方法计算92个有机分子均裂能的均方根误差从22.25 kJ/mol减少到1.84 kJ/mol,而MIV-BPNN方法使均方根误差减少到1.36 kJ/mol,可见B3LYP/6-31G(d)和MIV-BPNN联合方法可以提高均裂能的量子化学计算精度,并可预测实验上无法获取的均裂能值.     

GAUSSIAN程序中密度泛理论方法积分精度对计算结果的影响

给出了使用ＧＡＵＳＳＩＡＮ程序中密度泛函理论方法进行量子化学计算时遇到的一类问题－六氟锗乙烷分子Ｆ３Ｇｅ－ＧｅＦ３的基态构型随计算积分精度不同而改变,即ＧＡＵＳＳＩＡＮ程序中计算积分精度对计算结果产生重要影响的一个例子。     

统一统计理论多分割面热反应速率的计算程序

应用GAUSS积分方法，设计了建立在统一统计理论基础上的多分割面量子方法计算热反应速率的计算程序．通量积分N（E，S）基于内禀反应坐标（IRC）的信息采用阶梯函数量子数态法计算，由其微正则变分确定分割面．IRC信息由量子化学从头算方法得到．程序用FORTRAN语言编写．详细阐述了基本理论和程序算法及对H2＋H反应体系的成功应用．该程序可进一步适用于多原子分子的较大体系．     

价键理论的对不变式方法——Ⅱ. 无自旋价键计算程序Xiamen

发展完善了价键理论的对不变式方法,给出了对不变式的正则展开方法,并证明了对不变式可以展开成任意阶的子对不变式和相应余子式乘积的形式.利用对不变式方法,完成一个新的无自旋价键理论方法从头计算程序──Xiamen. 测试计算表明,Xiamen程序比基于传统价键方法的程序计算效率高,为量子化学计算研究提供了一个新工具.     

二氧化碳和丙烯直接合成甲基丙烯酸的NiPMo/TiO2催化剂的研究

用溶胶-凝胶法以磷钼酸(MPA)的镍盐溶液水解钛酸四丁酯制备了NiPMo/TiO2催化剂.使用ICP、 XRD、 TG-DTA、 IR、 TPD-MS和微反应技术研究了催化剂的化学组成、热稳定性、化学吸附性质和催化反应性能.杂多钼酸盐与TiO2通过O2-在TiO2表面发生了键合.在623 K下,杂多阴离子仍保持原有的Keggin结构.CO2在Lewis酸位Ni(Ⅱ)和Lewis碱位Ni-O-Mo的桥氧协同作用下生成CO2卧式吸附态Ni(Ⅱ)←O-(CO)←(O--Ni).丙烯有多种吸附态在催化剂上吸附.在563 K、 1 MPa和空速1500 h-1的反应条件下,丙烯的摩尔转化率为3.2%,产物MAA选择性为95%.     

Synthesis of 1-benzyloxypyrazin-2(1H)-one derivatives

Different approaches for the synthesis of 1-benzyloxypyrazin-2(1H)-one derivatives from simple amino acids have been investigated. A library of 33 precursors for the preparation of N-hydroxy pyrazinones was obtained in moderate to good yields.     

α-Amino acid derived enaminones and their application in the synthesis of N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates and other heterocycles

A new and simple synthesis of novel N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates, which exist in equilibrium with their 4-oxo tautomers, has been developed in two steps starting from N-protected α-amino acids. The key intermediates are enaminones, which can also be isolated, characterized, and used for the construction of other functionalized heterocycles, before they spontaneously decompose to pyrrole products. 4-Hydroxypyrroles are prone to partial aerial oxidation but can be efficiently alkylated or reduced to stable polysubstituted pyrrolidine derivatives.     

Specific intramolecular aromatic CH insertion of diazosulfonamides

The chemoselectivity in the intramolecular CH insertion of various diazosulfonamides has been experimentally studied. The results reveal that the aliphatic 1,4-, 1,5-, or 1,6-C(sp³)?H insertions of diazosulfonamides are not accessible, while the aromatic 1,5-C(sp²)?H insertion can be realized specifically by adjusting the diazo-adjacent group. In addition, the general chemoselectivities in the intramolecular CH insertions of diazosulfonyl compounds are summarized. Generally, diazosulfones undergo both aromatic 1,5-C(sp²)?H and aliphatic 1,5- and 1,6-C(sp³)?H insertions, while diazosulfonates undergo aliphatic 1,5- and 1,6-C(sp³)?H insertions. However, diazosulfonamides only undergo aromatic 1,5-C(sp²)?H insertion.     

A general and convenient synthesis of 4-(tosylmethyl)semicarbazones and their use in amidoalkylation of hydrogen,heteroatom, and carbon nucleophiles

A general synthesis of previously unknown semicarbazone-based α-amidoalkylating reagents, 4-(tosylmethyl)semicarbazones, has been developed. The synthesis involved three-component condensation of semicarbazones of aliphatic or aromatic aldehydes with the same or other aldehydes and p-toluenesulfinic acid. The scope and limitations of this reaction were investigated. The compounds obtained were demonstrated to be an efficient α-(4-semicarbazono)alkylating agents. They were reacted with H- (sodium borohydride), O- (sodium methylate), S- (sodium phenylthiolate), N- (pyrrolidine, sodium succinimide), P- (trialkyl phosphites), and C-nucleophiles (sodium diethyl malonate) to give the corresponding products of the tosyl group substitution, 4-substituted semicarbazones, including analogues of nitrofurazone. Among the prepared compounds tested in vitro for antibacterial and antifungal activity, three nitrofuryl-containing semicarbazones exhibited high biological activities with minimum inhibitory concentration (MIC) values of 8–32 μg/mL.     

Synthesis of novel chiral bidentate hydroxyalkyl-N-heterocyclic carbene ligands and their application in palladium-catalyzed Mizoroki–Heck couplings and asymmetric addition of diethylzinc to benzaldehyde

A small library of new chiral bidentate hydroxyalkyl-imidazolium salts 1 is conveniently synthesized on multi-gram scale from inexpensive and commercially available chiral pool amino acids. The corresponding carbenes, generated by deprotonation of imidazolium salts 1, in combination with palladium(II) chloride were tested in the Mizoroki–Heck coupling reaction. The most significant results in terms of yields and reactivities were achieved with low catalyst loading. The catalytic activities of these imidazolium salts were also investigated in the asymmetric addition of diethylzinc to benzaldehyde. The use of MgO nanoparticles as an additive in conjunction with these ligands played a crucial role in increasing the efficiency of these reactions.     

N-Heterocyclic carbene-palladacyclic complexes: synthesis,characterization and their applications in the C-N coupling and α-arylation of ketones using aryl chlorides

N-Heterocyclic carbene-palladacyclic complexes 3 were successfully achieved in a one-pot procedure under mild conditions. The structure of 3a was unambiguously confirmed by X-ray single crystal diffraction and it was an active catalyst in the Buchwald-Hartwig amination and α-arylation of ketones even at very low catalyst loadings (0.01?mol%).     

Toward new camptothecins. Part 6: Synthesis of crucial ketones and their use in Friedländer reaction

In the context of the preparation of camptothecin and luotonin A analogs, the synthesis of some key keto-precursors and their use in Friedländer condensation are described. This paper also focuses on the stability of these keto intermediates and emphasizes the major differences between indolizinones and pyrroloquinazolinones series. Noteworthy is also the report of some original structures isolated as by-products of some experiments.     

Iodine-mediated oxidative Pictet-Spengler reaction using terminal alkyne as the 2-oxoaldehyde surrogate for the synthesis of 1-aroyl-β-carbolines and fused-nitrogen heterocycles

An efficient iodine-mediated oxidative Pictet-Spengler reaction in dimethyl sulphoxide (DMSO) using terminal alkynes as the 2-oxoaldehyde surrogate for the synthesis of aryl (9H-pyrido[3,4-b]indol-1-yl)methanones is described. The scope of the protocol includes the total synthesis of Fascaplysin, Eudistomins Y₁ and Y₂. The methodology is extended for preparing pyrrolo[1,2-a]-quinoxaline and indolo[1,5-a]quinoxaline derivatives. The utility of 1-aroyl-β-carbolines was demonstrated by performing palladium-catalyzed β-carboline directed ortho-C(sp2)-H functionalization of the phenyl ring with thiomethyl (SMe) group using DMSO as source and for accessing 4-aryl-canthin-6-ones.     

Facile synthesis of bicyclic 1-arylpyrazol-5-ones

In this Letter, we described a facile method for constructing fused bicyclic 1-arylpyrazol-5-one ring system. We employed various methylene-containing carboxylic acids as the substrates and proved that the pyrazolone ring closure requires activated methylene group in intermediate II. Accordingly, a series of structurally diversified, fused bicyclic 1-arylpyrazol-5-ones was prepared in moderate to high yields using the requisite substrates.