100分求：计算化学类文献，要求，英文原文，部分翻译成汉语且翻译字数不少于3000字

Computational chemistry that can predict the spectra of a variety of compounds that cannot be obtained as

pure compounds was used to study the highly sensitive detection of bromate in ion chromatography Several

possible ions, molecules, and their complexes were constructed by a molecular editor, and optimized by

molecular mechanics (MM2) and MOPAC (PM3) calculations The possible electronic spectra of these

ions, molecules, and complexes were then obtained by the ZINDO (INDO)-Vizualyzer in the CAChe program

The lambda maximum (ìmax) of the spectra and the transition dipole were calculated using the ProjectLeader

program The comparison of the experimental and predicted results indicated that Br3

- was the probable

reaction product, and that NO2

- and ClO- accelerated the reaction

1 INTRODUCTION

Bromate is considered a carcinogen and the World Health

Organization (WHO) has recommended the provisional

bromate guideline value of 25 mg/L, which is associated with

an excess lifetime cancer risk of 7 10-5, because of the

limitations in the available analytical and treatment methods1

A highly sensitive analytical method was therefore developed

Bromate in ozonized water was detected with very

high sensitivity by ion chromatography with a postcolumn

reaction detection using ultraviolet absorption With the

addition of nitrite for the postcolumn reaction, the sensitivity

was improved 738-fold The detection limit was 035 mg/

L, and the linear range was >4 orders of magnitude, from

05 to 10 mg/L2 The addition of ClO- improved the

sensitivity 327-fold2

Chiu and Eubanks3 examined bromide spectrophotometrically;

they proposed a reaction mechanism and suggested

that the end product is tribromide3 The proposed reactions

are as follows:

In addition, bromate and chlorate were determined by

potentiometric titration after reduction with sodium nitrite4

Sodium nitrite was added in sodium bromide for the on-line

hydrobromic acid generator in this system, and highly

sensitive detection was achieved2 However, the reaction

mechanism and the final product have not been determined

Tuchler et al5 studied bimolecular interactions and directly

detected the internal conversion involving Br(2P1/2) + I2

initiated from a van der Waals dimer The reaction complex

was formed from a van der Waals dimer precursor, HBrâI2

The resulting product, highly vibrationally excited molecular

I2, was monitored by resonance-enhanced multiphoton

ionization combined with time-of-flight mass spectroscopy

The HBr constituent of the precursor HBrâI2 was photodissociated

at 220 nm The H atom departed instantaneously,

allowing the remaining electronically excited Br(2P1/2) to

form a collision complex, (BrI2), in a restricted region along

with the Br + I2 reaction coordinate determined by precursor

geometry Sims et al6 reported the fentosecond real-time

probing of bimolecular reaction Br + I2, and summarized a

number of trihalogen intermediates observed in matrix

isolation studies

Computational chemistry can predict the electronic spectra

of a variety of compounds that cannot be obtained as pure

compounds This tool was applied to study the highly

sensitive detection of bromate in ion chromatography

Several possible ions and molecules and their complexes

were constructed by a molecular editor, and optimized by

molecular mechanics (MM2) and MOPAC (PM3 and AM1)

calculations Their possible electronic spectra were then

obtained with the ZINDO (INDO/1)-Vizualyzer in the

CAChe program The lambda maximum (ìmax) of the spectra

of the transition dipole were calculated using the ProjectLeader

program The properties used for the calculation of

the molecular mechanics were bond stretch, bond angle,

dihedral angle, improper torsion, van der Waals, electrostatic

(MM2 bond dipole), hydrogen bond, and cut-off distance

for van der Waals interactions (900 Å) (van der Waals

interactions were updated every 50 interactions) The

parameters for the MOPAC calculation were geometry search

Author to whom correspondence should be sent

† Health Research Foundation

‡ Yokogawa Analytical Systems

Br- + 3ClO- f BrO3

- + 3Cl- (1)

BrO3

- + 5Br- + 6H+ f 3Br2 + 3H2O (2)

Br2 + Br- f Br3

- (3)

J Chem Inf Comput Sci 1998, 38, 885-888 885

S0095-2338(98)00084-5 CCC: $1500 © 1998 American Chemical Society

Published on Web 08/14/1998

options (precise, minimized by NLLSQ, optimized geometry

by BFGS), and properties [Mulliken population, energy

partitioning, polarizabilities, localize, thermo, rotational

symmetry (C1)] in the CAChe program The predicted data

were compared with those obtained experimentally

2 THEORY

According to the Lambert-Beer law, the ratio of the

intensity of the light of the inlet site (Io(î)) and the outlet

site (I(î)) is given by the following equation:

That is, absorbance A ) log10I/Io ) k(î)Dx, where the molar

extinction coefficient (molar absorption coefficient) I ) Io

10k(î)Dx, and k(î): molar extinction coefficient is the molar

absorptivity

The following equation is given as the relation between

absorption intensity as measured experimentally and that

estimated theoretically:7

The intensity of the spectrum is given by the following

equation:

where jájjköâerjiñj2 is the transition dipole

That is, molar absorptivity, k(î), is related to the transition

dipole The following parameters are found in eqs 4-7: D,

concentration of analyte; x, pass length of light; c, light speed;

N, Avogadro’s constant; h, Planck’s constant; V, frequency;

j, excited state; i, ground state; k, Boltzmann’s constant; er,

transition dipole moment; and kö, polarized light vector

3 RESULTS AND DISCUSSION

The computational chemical calculation was performed

by the CAChe program from Sony-Tektronix (Tokyo) using

a Macintosh 8100/100 personal computer The molar

absorptivity of several ions, molecules, and complexes were

directly measured on spectra obtained by ZINDO-Visualization

after their conformations were optimized by MM2 and

MOPAC (PM3 and AM1) Their transition dipoles were

calculated by the ProjectLeader program using MM2

and MOPAC (PM3 and AM1) The values of molar

absorptivity and the transition dipoles are summarized in

Table 1 The values of their complexes with nitrite and

chlorite are included The energy values of angle and van

der Waals obtained by the MM2 calculation are also given

in Table 1

The relation between the transition dipole and the molar

absorptivity was:

where Y is molar absorptivity (I/mol-cm) and X is the

transition dipole (debye) The chromatographic sensitivity

is directly related to the molar absorptivity of the analytes

The molar absorptivity of Br3

- and the Br2 + Br- complex

was very high, 190 000 The measurements of molar

absorptivity and the ìmax wavelength were not easily

obtained, but these values can be automatically calculated

using the ProjectLeader program The Br3

- and the Br2 +

Br- complex have similar structures, as shown in Figure 1

The complex between Br2 and Br- was automatically formed

after the optimization of the structure, and the heat of

formation energy value was the lowest among the analytes

listed in Table 1; the values were about -106 kcal/mol The

value of the complex was the same as that of Br3

- This

Table 1 Properties of Analytesa

analyte HOF, kcal/mol ìmax, nm td debye ma, L/mol-cm angle, kcal/mol vwv, kcal/mol

Br- -5600 - - 000 000

Br2 492 602 0277 81 000 000

Br3

- -10569 258 12300 188200 000 000

BrO3

- -3959 462 0927 595 328 000

NO2

- -4293 208 4005 24660 000 000

ClO- -3297 234 0409 458 000 000

Br2 + NO2

-/1 -9849 224 7227 74550 000 -026

Br2 + NO2

-/2 -10480 239 8183 91440 003 -005

Br2 + NO2

-/3 -9993 230 5550 43370 000 -022

Br2 + Br- -10569 258 12327 188250 000 -036

Br2 + ClO-/1 -11302 228 4758 30670 000 -033

Br2 + ClO-/2 -7452 228 10385 148400 000 -046

Cl- -5122 - - 000 000

Cl2 -1157 410 0464 336 000 000

Cl3

- -9106 214 10615 168200 000 000

Cl2Br- -9530 247 10727 148760 000 -032

Cl2 + OCl- -8751 243 5220 34 000 -036

BrO3

- + NO2

- -5111 209 4117 30166 000 -075

I3 -8558 221 12738 236800 000 000

I2Br -8759 229 12276 209360 000 000

a HOF: heat of formation (PM3); td: transition dipole; ma: molar absorptivity; angle: dihedral angle (MM2); vwv: van der Waals energy

(MM2); : molecule lacks electronic state information

Y ) 1057422X2 + 3017582X - 2368256

r2 ) 0993 (n ) 14) (8)

[I(î) Io(î)] ) 10-k(î)Dx ) e-ln10âk(î)Dx (4)

103âln 10âc

Nh

s k(î)

î

dî ) 8ð3

h2

jájjköâerjiñj2 (5)

f(theoretical) ) 8ð2mî

3h

jájjköâerjiñj2 (6)

k(î) ) 1

Dx

log10 I/Io µ jájjköâerjiñj2 (7)

886 J Chem Inf Comput Sci, Vol 38, No 5, 1998 HANAI ET AL

result indicated that Br3

- can be formed where Br2 and Brco-

exist as the BrI2 complex5,6

The question arises as to how NO2

- and ClO- acted in

the reaction: did these ions form different compounds or

complexes with bromide or bromine for the highly sensitive

detection of bromate The Br2 + NO2

- complex was

thusconstructed, and we optimized the structure by MM2

and PM3 calculations The Br2 and NO2

- formed three types

of conformations, as shown in Figure 2 The structures A

and B were obtained as molecules and the structure C was

obtained as a transition state Their energy values of heat

of formation are given in Table 1 as Br2 + NO2

-/1, Br2 +

NO2

-/2, and Br2 + NO2

-/3, respectively Their heat of

formation energy values were low; the lowest energy value

was -105 kcal/mol, about the same as that of the Br2 +

Br- complex The structure with the lowest energy value

is structure B in Figure 2 However, its molar absorptivity

was less than half of that of the Br2 + Br- complex This

result suggested that NO2

- may form a complex with Br2;

however, such a complex may not be the final product

because of the low sensitivity The ìmax wavelengths of

structures A, B, and C in Figure 2 were 224, 230, and 240

nm, respectively, and were different from that of the Br2 +

Br- complex and Br3

-, whose ìmax was 258 nm The ìmax

of 258 nm was the closest wavelength to that observed

experimentally (265 nm) This result also suggested that

such a complex may not be the final product The formation

of these complexes was supported by the negative values of

their van der Waals energy calculated by MM2 (Table 1)

Bromide did not form a complex with NO2

- Bromide,

bromine, bromate, and nitrite were not highly sensitive

analytes, due to their low transition dipole values and ìmax

wavelength

Another question was why the sensitivity measured in the

existence of ClO- was about the half of that measured in

the existence of NO2

- The reaction processes were estimated

according to the proposal of Chiu and Eubanks3

The value of molecular absorptivity of Cl2Br- (148 760) was

lower than that of Br3

- (188 200), and the ìmax wavelength

of Cl2Br- (247 nm) was also lower than that of Br3

- (258

nm) Therefore, the final sensitivity using ClO- as the

reaction reagent was less than that using NO2

-

Bromate formed a complex with nitrite; however, the

complex may be unstable due to the high energy value of

the heat of formation This complex is not a candidate for

the highly sensitive detection of bromate because of the low

transition dipole value and ìmax wavelength Bromine can

form a complex with ClO-; however, the energy value of

heat of formation was high for a complex with a higher

transition dipole This means that the Br2 + ClO- complex

may be not a candidate for the highly sensitive detection of

bromate The results just presented indicate that the highly

sensitive detection of chlorate and iodinate can be achieved

by using the techniques employed for the bromate analysis

The sensitivity of chlorate and iodinate will be 90 and 111%

of bromate; however, the ìmax wavelengths of Cl2Br- and

I2Br- are 10 and 30 nm lower, respectively, than that of

Br2Br- IfCl3

- and I3

- are the final products, the specific

ion generator should be constructed; however, the detection

wavelengths of Cl3

- and I3

- are further lower than those of

Cl2Br- and I2Br-, and the selective detection may not be

easy The computational chemical analysis of fluorate could

not performed due to the lack of stable electron stable

information for fluorate

An AM1 calculation can be used to optimize these

structures; however, the present AM1 calculation did not give

complex forms because of the fixed atomic distances The

ìmax wavelengths were usually shorter than that obtained

by PM3, and the values of molar absorptivity were smaller

For example, the maximum atomic distances of Br3

-

calculated by PM3 and AM1 were 5065 and 4575 Å,

respectively Their ìmax wavelengths and their values of

Figure 1 Electron density of the optimized structures of Br2 +

Br- complex and Br3

-

Figure 2 Possible conformations of Br2 + NO2

-

2BrO3

- + 4NO2

- + 4H+ f Br2 + 4HNO3 + 2H2O (9)

Br2 + Br- f Br3

- (10)

2BrO3

- + 4ClO- + 6H+ f

Br2 + Cl2 + 2HClO3 + 3H2O (11)

Br2 + Br- f Br3

- and Cl2 + Br- f Cl2Br- (12)可以预测有机混合物中一系列有机物色谱的计算化学能在离子色谱中进行溴离子的高灵敏度色谱分析。一些能测的离子，分子和他们的复合物分子结构能通过一个分子编辑器得到。再通过分子力学进一步优化和用MOPAC进一步计算来完善它,这些离子，分子和配和物的电子光谱就会在高度缓存程序中通过ZINDO (INDO)-Vizualyzer方法获得。那色谱和过渡偶极子的最大波长可以通过ProjectLeader程序计算出来。通过实验结果和预测结果的比较表明Br3-是可能的反应产物，而且其中的NO2-和CLO-加快了反应。

1 前言

溴酸盐被认为是一种致癌物子和世界卫生组织已建议它的含量准则为25mg/L，这与人一生超过710-5 的癌症发病率有关，这是由于以前溴酸盐在有效分析和处理方法上受到限制。因此，一种高灵敏度的分析方法就发展起来了。溴酸盐在溴氧水中通过离子色谱能被精确的检测到，而离子色谱是使用紫外吸收进行柱后反应测定的。随着亚硝酸盐在柱后反应中的加入，灵敏度提高了738倍。检测线035mg/L，并且从05-10mg/L的线性范围大于四个数量级，CLO-的加入也使灵敏度提高了327倍。

Chiu和Eubanks审查了甲基溴光度法，他们提出了一种反应机制，并认为那最终的产物是三溴化物。

此外，溴和氯在减少硝酸钠加入量后可通过电位滴定法测得，溴化钠中加入硝酸钠是为了溶液中出现氢溴酸，从而获得精确的测定结果。但是，反应的机制和最终产物仍然是没有确定。图兹勒等人研究双分子的相互作用和发现内部转换Br(2P1/2) + I2开始于范德华二聚体。那反应产物形成范德华二聚体，HBrI2。那最后产物是高聚物分子，他是通过共振性强的多光子电离法和质谱法相结合而测到的。那HBrI2的反应产物溴化氢的键长是220nm。氢原子的瞬间离开，使得其余的电子激发Br(2P1/2)，彼此发生复杂的碰撞，形成(BrI2)。在一个限制的区域伴随着Br- + I2同样取决于反应初始条件。Sims et al，他报告了双分子反应Br- + I2方面的探究结果，总结出了反应中间体在进行分离实验研究时能被观察到。

计算化学可以预测混合有机物中一系列有机物的电子色谱，计算化学还应用于精确检测离子色谱中的溴。一些可测的离子，分子和配合物的分子结构通过分子编辑器能被构造出来，再通过分子力学进一步优化和用MOPAC进一步计算。那么他们的电子色谱就会在高度缓存程序中通过ZINDO(INDO)-Vizualyzer方法获得。那色谱和过渡偶极子的最大波长可以通过ProjectLeader程序计算出来。计算化学中的程序还可以计算分子的键长，键角，二面角，扭转力，范德华力，静电力，氢键和由范德华力分离的距离（900 Å）。用MOPAC 计算方法计算的参数在下表1，并且各种特性都通过那CAChe程序显现出来了。然后，我们预测的数据就可以和这些实验得出的数据进行比较。

文献第三部分：

2 结果与讨论

计算化学的计算是由CAChe程序来完成的，这个程序是由东京的索尼泰克公司开发的，更适用于个人电脑。一些离子，分子和配合物的摩尔吸收率能在光谱中直接测量得到，而它们各自的光谱是离子，分子，配合物分子在经过进一步优化和计算后通过ZINDO-Visualization方法而得到的。那ProjectLeader程序用MM2和MOPAC方法可以计算它们的过渡偶极子。摩尔吸收率和过渡偶极子的测试值总结在表1中。它们的复合物如亚硝酸盐和亚氯酸盐的测试值也列在表1中。角度和范德华力的测试值通过MM2计算也被列在表1中。

摩尔吸收率和过渡偶极子的关系是：

Y = 1057422X2 + 3017582X - 2368256

r2=0993(n=14)(8)

其中Y是摩尔吸收率(I/mol-cm)，X是过渡偶极子(debye)。那色谱的灵敏度直接关系到样品的摩尔吸收率。Br3-的摩尔吸收率和Br2 + Br-配合物的摩尔吸收率都很高，大约是190000。摩尔吸收率和最大波长的大小是不容易测得的，但是这些值可以通过ProjectLeader程序自动计算出来。Br3和-Br2 + Br-配合物有类似的结构，如图1所示。

在Br3-和Br2 + Br-之间的复合物是在结构的优化中自动形成的，它能量中的热量值是上述表1样品中最低的。那测量值大约是-106kcal/mol那复合物的测量值是和Br3-的值一样的。这结果表明Br3-能形成诸如BrI2之类的复合物。

那么问题就归于了解亚硝酸根和亚氯酸根是怎样参与反应的：这些离子之间可以形成不同的化合物吗？或者由于溴的高灵敏度能与溴化物和溴酸盐形成复合物吗？Br2 + NO2-形成的配合物被构造出来，并且我们通过MM2和PM3计算来优化那结构。那溴与亚硝酸盐就可能有三种不同的构造，这些构造都列在表2中。

那A和B是获得的分子，而C是过渡态。它们的热量值分别列在表1中。它们的热量值都很低，其中最低的能量值是-105kcal/mol,这能量值是和Br+Br-的能量值一样的。在表2中可以知道最低能量值的构造是B化合物的结构。然而，它的摩尔吸收率比Br2 + Br-复合物的一半还少。这结果表明亚硝酸根能和溴形成复合物；然而，由于那低的灵敏度得知这种复合物不是最终产物，A,B,C的最大波长列在表2中，一次是224，230和240nm。显然，这是和Br+Br复合物不同的。那最大波长258nm最靠近那理论波长265nm。这结果也表明了那产物不是那最终产物。这些复合物的范德华力通过MM2和PM3计算得知是负值列在表1中。溴化物不能和亚硝酸根形成复合物。溴化物，溴酸盐，溴离子和亚硝酸盐都不是高灵敏度样品，这是由于他们的最长波长和过渡偶极子决定的。

用内置函数optim()optim(par,fun,lower,upper,method)大致用到这5个参数par是初始值，你选离你峰值差不远的xfun是生成你正弦波的函数lower和upper定义域method用"BFGS"牛顿迭代法，或者"L-BFGS-B"升级版牛顿迭代法。以下是得到的结果，我用f(x)=x^2-2x+1试了以下>optim(3,fun,lower=-5,upper=5,method="BFGS")$par[1]1#x值$value[1]0#y值$countsfunctiongradient#不知道是什么4444$convergence[1]52#算了多少次收敛

>

用内置函数 optim()

optim(par,fun,lower,upper,method) 大致用到这5个参数

par是初始值，你选离你峰值差不远的x

fun是生成你正弦波的函数

lower和upper定义域

method用 "BFGS"牛顿迭代法，或者"L-BFGS-B"升级版牛顿迭代法。

以下是得到的结果，我用f(x)=x^2-2x+1试了以下

>optim(3,fun,lower=-5,upper=5,method="BFGS")

$par

[1] 1 # x值

$value

[1] 0 # y值

$counts

function gradient # 不知道是什么

44 44

$convergence

[1] 52 # 算了多少次收敛

个人感觉你的INCAR不太适合做NEB

根据vtstcode的说明 我觉得这个INCAR比较合理 收敛也会比较快 主要

的区别是用了global lbfgs method（IOPT=1）去优化反应路径

如果觉得自己的初始guess比较好的话 可以将invcurv提高到005

或者先用001做几步 然后用新的初始路径提交并将invcurv提高到005

其他的没什么了 就是把一些默认值写出来 感觉更清楚一点

另外优化一般vasp计算速度的参数也尽量加

比如LPLANE=TRUE ;NSIM=4

试试看

ENCUT = 480 !经过优化的最小数值,文献最高取500

NPAR = 2

LPLANE=TRUE;NSIM=4

NELMIN = 5

EDIFF = 1E-4

EDIFFG = -005

LREAL = Auto

NSW = 60

GGA = 91

IBRION=3

POTIM = 00 !经过多次测试计算,感觉比较合理

ICHAIN=0

IMAGES = 3

SPRING = -5 ! NEB 方法

LCLIMB=TRUE

IOPT=1 #global lbfgs method

LGLOBAL=TRUE

MAXMOVE=02 # max step

INVCURV=001 # initial curvature

ISMEAR =0

VOSKOWN =1

PREC = Accurate

:D

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