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ghui

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[資源] 憶起過(guò)往事，滿是辛酸淚——JACS接收前的心路歷程已有21人參與

憶起過(guò)往事，滿是辛酸淚——JACS接收前的心路歷程
作者：高輝

寫在前面的話：文章剛剛被化學(xué)領(lǐng)域最重要最有影響力的期刊JACS（Journal of the American Chemical Society，美國(guó)化學(xué)會(huì)志）接收，欣慰之余，將其中的心路歷程撰寫如下，以此作為對(duì)小木蟲(chóng)以及廣大蟲(chóng)友們的回報(bào)，但有一二對(duì)蟲(chóng)友們有益者，也不枉此辛！當(dāng)然我沒(méi)有忘記，我仍然是個(gè)小菜鳥(niǎo)，仍然需要向同行們學(xué)習(xí)，歡迎蟲(chóng)友們跟我交流，讓我們共同進(jìn)步吧！

多少次夜靜人稀的校道上踽踽而行？

多少次睡眼惺忪掙扎著爬出被窩去打開(kāi)實(shí)驗(yàn)室的門？

多少次心浮氣躁坐立不安欲哭無(wú)淚？

多少次不堪重負(fù)恍若絕境看不到一丁點(diǎn)光明？

多少次沉默了親人的問(wèn)候？多少次怠慢了朋友的通信？多少次推延了同學(xué)的邀請(qǐng)？

多少次春節(jié)沒(méi)有回家度過(guò)？多少次聚會(huì)或者活動(dòng)沒(méi)有積極參加？

多少次身邊的良辰美景錯(cuò)失？多少次重要的機(jī)會(huì)沒(méi)有好好把握？

多少次在圖書館的書架前被震撼？多少次精彩的演講沒(méi)有去聽(tīng)？

多少次滿懷期待終成幻夢(mèng)？

多少次鄭重承諾化為泡影？

……

日復(fù)一日，年復(fù)一年，歲月到底不饒人，如今將要步入而立之年卻怎么都立不起來(lái)？充斥著無(wú)奈壓抑著倔強(qiáng)依然孑然一身，功不成名不就老大不小了還要家人操心，年少輕狂的所謂抱負(fù)早已消失了影蹤，接受著共和國(guó)的洗禮卻咒罵著現(xiàn)實(shí)的不平，愛(ài)國(guó)兄弟的諄諄教誨卻怎么也起不了作用，一邊窮困，一邊憤青……

終于，否極泰來(lái)不再是夢(mèng)，JACS的認(rèn)可使我此刻成為最幸運(yùn)的人。

那是二零零六年的秋冬，那時(shí)林志強(qiáng)老師的專英要求用英語(yǔ)講自己的化學(xué)研究presentation，那時(shí)我在學(xué)術(shù)上一無(wú)所有，除了滿腔的熱情，那時(shí)柯卓鋒師兄給了我一篇當(dāng)年的JPCB和一篇CR，“就拿去講這個(gè)吧”，都是關(guān)于磷酸酯水解的論文。那是二零零七年的開(kāi)春，方冉師兄的一次文獻(xiàn)查新得到一篇尚沒(méi)有頁(yè)碼的剛剛在JACS刊出的金屬單鋅配合物催化磷酸酯水解機(jī)理的研究論文。從此堅(jiān)定了我摸索深入下去的決心。摸索，不停地摸索，嘗試，不停的嘗試，無(wú)數(shù)次的失敗，無(wú)數(shù)次的雜七雜八的事情，卻并沒(méi)有動(dòng)搖我繼續(xù)摸索下去的決心。因?yàn)樵阶呦氯ピ接X(jué)得自己的無(wú)知渺小，正所謂學(xué)無(wú)止境。此后，柯卓鋒師兄的出國(guó)留洋一年，也正是我雜七雜八甚至馳騁三國(guó)游戲的一年，期間算了兩個(gè)月葉保輝老師的水簇，無(wú)果，后葉發(fā)了JACS，據(jù)說(shuō)當(dāng)時(shí)若能計(jì)算出來(lái)的話是準(zhǔn)備發(fā)Science的，無(wú)奈我當(dāng)時(shí)太水太嫩。期間更是算了半年甚至將近一年的Sm卡賓環(huán)丙烷化反應(yīng)，終覺(jué)無(wú)趣，有數(shù)據(jù)卻未成文，亦屬無(wú)果。轉(zhuǎn)眼間二零零八年的秋冬到了，我也正式博士了，雙鋅配合物催化磷酸酯水解機(jī)理的最新實(shí)驗(yàn)研究正好剛出來(lái)，這正是我所期盼的，我也從此前的單鋅摸索告一段落，磷酸酯的計(jì)算仍然停留在HF/3-21G水平。零八年十二月的博士開(kāi)題報(bào)告雖然有了一些初步的思路，也著實(shí)有一點(diǎn)點(diǎn)初步結(jié)果，但這遠(yuǎn)遠(yuǎn)不夠，……繼續(xù)摸索，其中的艱辛又豈是只言片語(yǔ)所能概述？跟我一起上研讀博的人好幾個(gè)都已經(jīng)早早發(fā)了文章，得了獎(jiǎng)學(xué)金，已無(wú)畢業(yè)壓力，只需做自己喜歡做的事情，而我卻還在壓力之下艱難前行，在零九年七月柯師兄去日本前完成初稿，到一零年七月份投稿到JACS，整整修改了一年，這一年過(guò)得太過(guò)漫長(zhǎng)太過(guò)辛勞。沒(méi)辦法，這是我寫的第一篇文章，而且又是要投JACS的，在與柯師兄和Nathan幾次郵件后，硬是憋啊憋，改啊改，總算最終完稿。

下面是JACS審稿修改全記錄：

2010.7.29 投稿到JACS

2010.8.19 第一次修改意見(jiàn)返回，四個(gè)審稿人，其中前兩個(gè)審稿人建議小修改發(fā)表，后兩個(gè)大修改后再審

2010.10.17第一次修改稿發(fā)出去（沒(méi)辦法，根據(jù)審稿人的意見(jiàn)又算了將近兩個(gè)月）

2010.11.7第二次修改意見(jiàn)返回，第四審稿人完全同意，第三審稿人卻認(rèn)為我們的回復(fù)沒(méi)有重視他的意見(jiàn)

2010.12.12第二次修改稿發(fā)出（又算了一個(gè)月，教訓(xùn)啊：審稿人的意見(jiàn)再怎么重視都不過(guò)分，謹(jǐn)記�。�

2011.1.6 第三次修改意見(jiàn)返回，（在經(jīng)歷了一個(gè)漫長(zhǎng)的焦慮等待后忐忑的心總算有了點(diǎn)慰藉了，全是TOP5）

2011.1.9第三次修改稿發(fā)出

2011.1.10JACS接收

回顧整個(gè)拉鋸戰(zhàn)過(guò)程，我必須向這四位審稿人致以最崇高的敬意，他們都是這個(gè)領(lǐng)域最最頂尖的科學(xué)家（其中至少有三位可以確定是我推薦審稿人里的六位牛人中的，推薦審稿人也是一門學(xué)問(wèn)，呵呵，要知道，我極不情愿把這些德高望重的牛人們與國(guó)內(nèi)很多披著學(xué)術(shù)外衣的商人們放在一起，那樣是對(duì)這些科學(xué)良知的人的褻瀆），而我這個(gè)小菜鳥(niǎo)，能得到他們的指點(diǎn)，從而使得文章更加Perfect（盡管多算了好幾個(gè)月，盡管提心吊膽戰(zhàn)戰(zhàn)兢兢了好幾個(gè)月）。

以下是JACS的總的評(píng)審結(jié)論匯總：

Reviewer: 1
Significance: High
Novelty: Moderate
Broad interest: High
Scholarly presentation: High
Are the conclusions adequately supported by the data?: Yes
Are the literature references appropriate and correct?: Yes
Do the contents justify the length of this manuscript?: Yes

Reviewer: 2
Significance: High
Novelty: High
Broad interest: High
Scholarly presentation: High
Are the conclusions adequately supported by the data?: Yes
Are the literature references appropriate and correct?: In Part
Do the contents justify the length of this manuscript?: Yes

Reviewer: 3（第三次評(píng)審結(jié)論）
Significance: Top 5
Novelty: Highest (top 5)
Broad interest: Highest (top 5)
Scholarly presentation: Highest (top 5)
Are the conclusions adequately supported by the data?: Yes
Are the literature references appropriate and correct?: Yes
Do the contents justify the length of this manuscript?: Yes

Reviewer: 4（第二次評(píng)審結(jié)論）
Significance: High
Novelty: High
Broad interest: High
Scholarly presentation: High
Are the conclusions adequately supported by the data?: Yes
Are the literature references appropriate and correct?: Yes
Do the contents justify the length of this manuscript?: Yes

以下是JACS的總的評(píng)審意見(jiàn)匯總：

審稿人一：

This paper reports the results of a density functional computational study of the mechanism of phosphate diester cleavage catalyzed by a dinuclear Zn(II) complex. These calculations use a polarizable continuum model to estimate solvation energies for the charged catalyst and reactants. I am not qualified to comment on the quality of the calculations. However, the computational modeling of this metal-ion complex catalyzed reaction presents a very difficult challenge, and I suspect that the author's apparent success is a significant achievement. In addition, the authors have an excellent understanding of earlier experimental studies on these metal ion complexcatalyzed reactions. The agreement between the calculated and observed barrier for the catalyzed cleavage of 2-hydroxypropyl-4-nitrophenyl phosphate is evidence that these calculations provide a true structure for the reaction transition state. In addition, the computational results provide an interesting structure for the Michaelis complex and insight into the reaction mechanism not obtained in experimental studies. This work will attract the attention of computational, organic and inorganic chemists interested in reaction mechanisms.

Publication in JACS is recommended, subject to the author's considerations of the following comments and questions.

審稿人二：

This manuscript reports a DFT computational study of the hydrolysis of the phosphodiester HpPNP by a binuclear zinc catalyst for which a series of physical organic experimental studies provided data suggestive of a concerted mechanism. The authors’ calculations support that conclusion, as well as the proposals regarding the protonation state of the active species. The abundance of experimental data make this a good system for a computational analysis, and the calculations reproduce the experimental results reasonably well. New insight comes from the nucleophile 18O KIE, which supports the idea that HpPNP binds to the catalyst with the nucleophile hydroxyl group coordinated to one of the zinc ions, and is subsequently deprotonated. This study thus gives a more concrete picture of the binding mode of the substrate to the catalyst than could be determined from experimental results. The binding mode of substrates to dinuclear metallophosphatases, and even to their small molecule model systems, remains an area of considerable uncertainty.

Publication is recommended after minor revisions are made.

審稿人三：

第一次審稿意見(jiàn)：

In this MS the authors describe a DFT study on the cleavage of 2-hydroxypropyl pnitrophenyl phosphate (HpPNP) promoted by a dinuclear Zn(II) catalyst which wasexperimentally studied extensively by Richard and Morrow. The main findings of thiscomputational study are that the lowest energy computed pathway for cleavage ofHpPNP involves double activation of the phosphate by binding to the complex in a Zn(II)—O-P-O—Zn(II) motif, followed by an equilibrium deprotonation of the hydroxypropyl group to form a Zn(II) associated 2-oxypropyl nucleophile which thennucleophilically attacks the phosphoryl unit in a concerted displacement of the pnitrophenoxy group. This pathway fits the mechanism favoured by Richard and Morrow, and supports additional heavy atom kinetic isotope effect studies by Hengge and Richard and Morrow. In addition the authors have computed a less favoured pathway for a stepwise reaction whereby additional waters coordinated to the catalyst displace the phosphate binding from two Zn(II) ions to one Zn(II) ion, with a H-bonding network to the other. This pathway has a general catalysis for the proton transfer with concurrent attack of the 2-oxypropyl group on the P to form a 5-coordinate phosphorane intermediate with subsequent fast departure of the phenoxide leaving group. Overall this is has the makings of a good paper where the computational results on a fairly well-defined system fit with what is known experimentally, and the computation does add to what we know about that system. I have some points that would make the MS clearer and more precise with the presentation.

第二次評(píng)審意見(jiàn)：
跟Fan and Gao的那篇物理化學(xué)的報(bào)道的路徑的比較
減少NBO分析的權(quán)重

第三次審稿意見(jiàn)
This is a vastly improved presentation of what is certainly an important contribution to the literature pertaining to a two metal ion catalyzed cleavage reactions of phosphodiesters as models for metallonuclease catalyzed processes. I read this version with interest, in particular the nice presentation of the effects of the various additional calculation parameterization which clearly lead to important energy differences between the methods. I am now happy with the conclusions made, and in particular a more careful comparison of the general-base process of Fan and Gao with the concerted process here, when calculated by methods with the same parameterization. The ms can be published essentially as is, but the authors might like to consider the following three points.

審稿人四：

第一次評(píng)審意見(jiàn)：
The authors use DFT calculations to investigate the mechanism for the cleavage of an RNA analogue HpPNP catalyzed by a dinuclear Zn(II) complex Zn2(L2O). The authors identify a plausible cleavage mechanism, which is a fairly routine task with quantum chemical methods. Meanwhile, the authors fall short when characterizing the role of the catalyst, which would have a significant impact in the context of catalyst design. As such, the study is not suitable for publication in JACS in its present form, but may be suitable for other ACS journals. That being said, if a more thorough analysis of the role of the catalyst was performed, and the manuscript was modified accordingly, the study may become suitable for publication in JACS. I would encourage the authors to attempt this route, and provide the following comments regarding the analysis of the mechanism and role of the catalyst.

第二次評(píng)審意見(jiàn)：
The authors have addressed main point of my previous comments regarding the need for a detailed discussion of the role of the catalyst (comment 1 in my previous report) by adding a section devoted to this purpose. As such, I believe the manuscript is now in sufficient form for publication in JACS.

[ Last edited by ghui on 2011-1-24 at 16:56 ]

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[資源] 憶起過(guò)往事，滿是辛酸淚——JACS接收前的心路歷程 已有21人參與

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